Traitors of the Stars: Genesis
by Lord-Druid
Summary: The prequel to Traitors of the Stars. Behold the untold adventure of Shinji Ikari to find the secret of the Blue Water.
1. Where It All Began

_Disclaimer: Evangelion and the Secret of Blue Water belongs to Gainax. Paranoia Agent belongs to Madhouse._

* * *

 **Traitors of the Stars: Genesis**

 **Chapter 1: Where It All Began**

 _Tokyo-2: 2004_

Keiichi Ikari was your everyday by-the-book kind of cop. During interrogations of criminals he usually plays the bad cop, while his partner, Mitsuhiro Maniwa, played the good cop. But there was a case so insane, more crimes were committed then they were able to catch up. The only thing that they knew was that all of the crimes were connected to the one everyone will call 'Lil' Slugger'. His wife, Misae, died sometime before it was over and he doesn't know what happened to Maniwa after that. After the case, the city of Tokyo-2 was in shambles. A military organization called SEELE came out of nowhere and fixed the destruction. making them heroes to the people of Tokyo-3.

* * *

 _Tokyo-3: 2005_

One year has passed since that insane event. Keiichi was a regular security guard, which is quite the downgrade considering his past job. While leaving his job, he found a child, a girl with dark skin. He thought she was with a tourist family. She looked lost. He approached her.

"Hi there." He said to the girl.

The girl looked at him in a friendly manner. "Hello."

"Are you lost?" He asked.

"No." She said.

"Are you with anyone?" He asked.

Her smile turn into a frown. "No." He asked if there was anyone she knew around here. "I don't have anyone anymore."

'She's an orphan?' he said to himself. Feeling sorry for her, knowing what it's like to be alone. "Come with me. Until we find someone around here you can stay until then."

"Yes, sir." The girl smiled.

"Do you have a name?" Keiichi asked.

"Nadia. That's my name." She said.

* * *

 _Ikari Residence_

"There are some others here. Including my nephew, Shinji. He's a little shy though. He may even act a little strange." He looked at her before walking in the house. "But I really hope you two will get along. Even if he doesn't think so, he needs friends."

"Yes, sir." Nadia nodded.

Keiichi knocked on the door. A woman opened the door. "Keiichi! It's good to see you." the woman said.

"Hello, Yui." Keiichi said to the woman.

She notices Nadia. "So, who is this pretty little lady?" She asked.

"Her name is Nadia. She looked lost so I asked if she was with anyone or if she knew anyone here." Keiichi explained.

"I'll call them, do you know their phone number?" She asked him.

"I don't think that would be a smart idea." he said.

"Why?" She asked, causing Keiichi to be stricken with grief.

"I think you know the reason." He said.

"Oh, I am so sorry, Nadia." She bend a knee to meet her eye to eye. "My name is Yui Ikari."

Nadia smiled. "Hello, Miss Ikari."

Yui smile "I have a son, his name is Shinji. He might be able to play with you. It's been a while since he had friends."

"Yes, ma'am." Nadia nodded.

"I'll show you to his room." Yui offered.

"I would also like to talk to you." Keiichi said as Yui lead Nadia upstairs to Shinji's room.

Yui knocked on a door that lead through Shinji's room. "Shinji. I have someone here who'd like to meet you."

Shinji opened up the door to see his mother and a girl. "Hello." Nadia said to him.

"Nice to meet you." Shinji said to her.

"Would you mind keeping her company while your uncle and me talk?" She asked her son.

"Sure." he hesitated as he said to her as she left.

"So, what do you do for fun?" Nadia asked.

"Depends on what you mean. I actually spent my time playing my PS2. My favorite game is Shin Megami Tensei III." He showed her his library of games.

"Can I play it?" she asked.

"Are you sure you want to play that one. I mean go right ahead, but that game is suppose to be hard." Shinji warned her.

"Than teach me through it." Nadia said as Shinji sighed.

Keiichi sat on the kitchen table as Yui came back. "I thought you would be smoking up a storm when I got back."

"Disappointed?" he chuckled.

"Surprised is more like it." she laughed.

"Things have changed." he sighed as he stretched his arms.

"Yes. I'm still sorry about everything that happened." Yui said sincerely.

"Why? You weren't there when it happened. It wasn't your fault." Keiichi said.

"But why is she here? You're not intending to adopt her are you?" Yui asked.

"I'm considering it." Keiichi admitted.

"I understand. You always wanted a daughter didn't you?" Yui asked

"Yes, and this girl is all alone. I can't just leave her somewhere, where others would just walk past her or treat her wrong." Keiichi passionately said to his sister.

"I understand. If you want to adopt her, then you have my support. I'll tell Gendo about it when he comes home." Yui assured him. "You two were good friends for the longest time. If anyone will have your back, it's us.

"Thanks, sis. I'll think this through." He said as he gave her a hug.

"She can sleep here for a while until things get straightened out." Yui offered.

"Thanks again, I was hoping her and Shinji get along with each other." Keiichi said. "He does need a friend."

He left some time after the conversation. "I better tell the kids." she went upstairs to Shinji's room.

"Shinji." She knocked on the door as she opened it. "Good to see you two getting along. Uncle Keiichi is going home so Nadia is going to stay here until further notice."

"I understand, Mother." Shinji said as she leaves.

Nadia couldn't help but smile. "I hope this is a beginning of a beautiful friendship."

"I really hope so, too." Shinji said hesitantly.

* * *

 _Tokyo-3: 2015_

Much has happened after ten years. Keiichi officially adopted Nadia, both Gendo and Yui were hired by SEELE and Shinji is training to follow suit. Every year, Keiichi and Nadia went to another nation, and every-time she left, Shinji would feel down. But, even that did not attempt to slow him down. Keel Lorenz, who was the leader of SEELE, hired Kozo Fuyutsuki as Shinji's personal trainer.

Fuyutsuki taught Shinji everything. How to shoot a gun. How to properly use a knife in combat. How to blend in with the environment. After training, he was told to report to Lorenz for his first mission. "Shinji Ikari. I am pleased with your work as a progressive member of the training camp. I would be happy to welcome you to SEELE. But before you are officially a member, you must find a special type of jewel, very rare."

He showed him the picture of a sapphire, shaped like a diamond. 'That's Nadia's jewel.' he thought to himself. 'Why would they want this?'

"It was last seen in France. Do whatever means necessary to get that jewel. You don't want to make me disappointed, you wouldn't like me when I'm disappointed. Now go and don't even think about coming back without the jewel." Lorenz ordered him.

"Yes, sir." He left to prepare for the mission, but was stopped by his father.

"Good to see you, Shinji." Gendo said as he patted Shinji on the back. "It's good to see you have become a member of SEELE."

"Well, I'm not an official member yet." Shinji said cautiously. "I still need to do one more thing for General Lorenz."

"Of course." he said as he sighed. "What does he want this time? A book he wants to read in his spare time? A movie he wants to watch? A yacht so he can relax?"

"He actually wants a special kind of jewel in France." he laughed.

"A jewel? In France? He probably wants to get it for an anniversary or something and he's to lazy to get it himself." He whispered to him. "Don't tell anyone I said that."

"Of course." Shinji said smiling.

"I'll leave you to it then. Make sure you give your cousin a visit while your there. I'm sure she will be very surprised." Gendo said as he walked away.

Shinji contemplated whither he should steal it from under her nose or just ask her flat out. 'If I steal it, she would hate me forever. But if I tell her straight out, she'll probably decline. Considering she was wearing it since we met, the former maybe the best course of action. I could just get a fake one... No, they have the best jewelers and that would be lectures from Fuyutsuki all over again. What should I do.'

"Feeling under the weather?" Fuyutsuki asked causing Shinji to jump. "Calm down. I came to give you words of wisdom. I had to go get a set of armor in a forest in England, somewhere to get where I am. I ultimately found it, but damn, did I had to hunt for that set. In comparison, your getting off easy."

Shinji laughed. "I bet I am. But I'm still a little uneasy. What if I mess up? I trained my life for this."

Fuyutsuki saw that he was hesitating. He put his hand on his shoulder. "You can do it. No matter what happens, I believe in you." He said as he left. "Good hunting."

Shinji knew just what to expect. 'I just hope I do the right thing.'

* * *

 _Paris-5_

Shinji looked around the city looking for his cousin. "If she's just visiting, she's bound to be in a hotel or something. The question is 'which one'?" He said to himself. "The western side of the city is more likely where they would be, since the annual parade is starting around here."

"Excuse me." He turned around to see a boy with a strong accent. "Are you Shinji Ikari?"

'How does he know my name? Has Nadia made a friend already?' Shinji thought to himself before speaking. "Yes."

"I thought so. You look just like she said." said the boy.

"She?" Shinji asked.

"Yes. Nadia Ikari. I swear it was picture perfect. Though looking closer you two do have some resemblance." he said.

Shinji chuckled "Yeah, I guess so. Anyway do you know where she is staying right now?"

"Yes, actually she's staying at the Round Table Hotel. Between the Arc de Triomphe and the Eiffel Tower. I'll mark it on your map." the boy put a red dot on the location on Shinji's map.

Shinji was overjoyed. "Thank you... I'm sorry I don't think I asked for your name."

The boy smirked "Don't mention it. My name is Jean Rocque Raltique, but you can call me Jean."

"John?" Shinji said, unsure of his name.

"No, Jean." he said.

"If you say so. Well, thank you again, hope to see you again someday." Shinji said to him as he left.

Jean waved to him. 'He is such a nice guy. I can see why she idolizes him so much.'

* * *

 _Round Table Hotel_

Upon entering the hotel, Shinji saw two men in white suits, one of them was short and fat, while the other was tall and skinny. 'Great, the Mario Brothers actually joined a Mafia.' Shinji joked to himself going to the front desk.

"Hello. How can I help you?" The woman in the front desk asked.

"Hi. I'm here to visit a current resident here. Keiichi Ikari." Shinji said.

"Yes, we have him here. Room No. 111." Said the woman.

"Thanks." Shinji said. He went down the hall to the room. He knocked on the door. "Hello, Uncle Keiichi! Nadia!" he waited for a minute before knocking again. 'No answer. Maybe they're out somewhere.'

He went back to the front desk. "Hello, sir. Is there a problem?"

"No. I just came while they're out." he told the woman at the front desk. "If you see him, tell him that Shinji Ikari was here."

"Sure thing." Shinji left the hotel.

'Sucks that they're not here. But they couldn't have gone to far.' Shinji thought to himself as he walked down the road. 'Maybe I'll watch a movie or something and maybe I'll watch a movie or something. Kill some time.'

Suddenly, he was captured by the two men in white. "What do we have here, Sanson?" The tall one asked.

"A maggot to bait fish with." The short one said. "Let's get him to the boss, Hanson." They blindfolded and gagged him as they tied him up.

* * *

 _?_

They removed the blindfold from his face. "Looks like the boss ain't here yet." Sanson said, sounding disappointed. "Shame, the boss would have love to have a guest. Especially one who would benefit the plan."

Hanson entered his sight. "For the time being I want you to tell us what we want to know." Sanson removed the gag.

"What, that you have bad taste in clothing design. Who uses bowties anymore? Were they ever popular?" Shinji laughed.

"That's enough. You will tell us about this jewel." He said as he showed a picture of the same sapphire that Nadia has to Shinji.

'Intel dropped the ball on this one. Lorenz never said anything about competitors.' Shinji smiled. "Go to a jewelry store. They're bound to have something like that."

They got angry. "You little shit."

"That's enough." came a female voice. "I will take care of this. Why don't you go play your games."

"Yes, Ma'am." They left after saluting her.

The woman came from the shadows. She look like a military general. A red uniform to match her red hair. "You must forgive those two. They have a funny way of saying 'hi'." Shinji stared at her intently. "I see you don't think highly of me. Do you know who I am?"

"Nobody cares, Matriarch." Shinji said.

"Matriarch? Don't tell me you thought we were a mafia. We're not like that." The woman laughed.

'They're not Mafia men? Thank God, I thought I really needed to do some improvising.' Shinji sighed.

"Though I'm impressed. You had the balls to stand up to two men in suits. How about joining us?" she offered.

'This could be my chance. I'm willing to bet these guys are the 'honor among thieves' types.' Shinji thought. "I'll be willing to tell you anything. If you take these bindings off."

* * *

 _AN: Thank you to everyone. I hope you enjoy this prequel._


	2. Peace and War

_Disclaimer: Evangelion and Secret of Blue Water belongs to Gainax. Paranoia Agent belong to Madhouse._

* * *

 **Traitors of the Stars: Genesis**

 **Chapter 2: Peace and War**

 _Paris-5, ?_

"Okay, guys. Here's what we're going to do." the woman said to Shinji and her two henchmen, showing piectures in the meantime. "This is the jewel we are going to capture. It's around the neck of this girl. We are going to get it by sneaking into her room in the Round Table Hotel and taking it from her while she sleeps." she point to Shinji. "This boy demonstrated incredible sneaking tactics. So, I'm appointing him as the man who can do this. We will execute the plan at midnight exactly. We are getting a large sum of money, so do not mess this up." She then looked at Shinji. "Do well, and I will make sure you have your fair share. I already have a room key for you, so you have no excuse to not get it."

'A large sum of money. If one is SEELE, who's the other who wants this?' Shinji thought to himself. 'It doesn't matter. All I have to do is steal it and leave these guys in the dust.'

* * *

 _Round Table Hotel, Midnight_

Shinji entered the hotel and went to the front desk. He saw a man in the front desk. "Excuse me. I'm here to visit Room No. 111."

"Okay. Want me to call them up and tell them your coming?" the man asked.

"No, I want to surprise them." Shinji said before leaving the front desk to the room he was looking for.

"Are you close to the room?" he heard on the walkie-talkie.

"Yes." Shinji smiled. "Rest assured I will make whatever your getting worth it."

"Understood. Rendezvous to the Notre-Dame after your done. Out." the voice on the walkie-talkie said.

"Roger that. Out." Shinji said. 'I really hate those guys. Not to mention, these things are ancient. Where did they get this thing?'

He reached the door to the room and used the key card. He slowly opened the door to see that the lights are out. 'They might be asleep already.' he put his communicator to night vision and sneaked to the bed where the snoring was. 'She always snored while she was sleeping.' She was laying on her back. 'That's really convenient.' he told himself. He saw the necklace around her neck and carefully undid it. He finally got it, only to find out that it was an emerald, not even a real emerald, it was a fake.

He turned on the lights to see the beds. All of them were empty save the assorted items made to look like they were on the bed. "Christ."

A voice came from the walkie-talkie. "Hello, are you there?" The voice said.

"Yes." Shinji said.

"Good. Abort the mission. We have them." The voice said.

"I hope you said your peace." Shinji said smirking.

"What are you talking about?" they asked.

"Your clients can keep the money. I'm getting something more than just money." Shinji said. "I can get it with or without you."

Shinji left to the streets and saw his uncles car. "Get in." he heard his uncle yell. He entered the car to find his cousin and the boy from earlier.

"If you were going to warn them, worry not." Jean told him.

"Jean told us that you were kidnapped. I'm surprised your here at all, actually." Nadia told him.

"I'm sorry I had to pop in unannounced. Thank you, Sean, for keeping them save." Shinji said.

"It's Jean." Jean corrected him.

"There's a weird tank-like thing coming after us. We have to find a way out of here!" Keiichi told him.

Shinji looked behind him. "Oh my God, that can't be real." he saw a huge sphere-like tank with mechanical arms. 'That looks like a SEELE model, but something seems off. Are they the ones supplying them?'

"I may have something." Jean said as he took out a bottle rocket and a lighter. "I'll just have to aim it right, and fire when ready."

"That's insane!" Shinji said.

"If that wasn't the case. This won't work." Jean said smiling as he lighted the bottle rocket, and aimed out the window. "Steady."

"There's a turn coming up!" Keiichi said.

"Steady." The sparks from the fuse went inside the rocket. "Gotcha!" He let go of the firework as it went inside the tank. The tank exploded as they made a turn.

Far from the chaos, the leader of the thieves were in a rage. "Dammit! She got away from us again! That's the second time that's ever happened! These old SEELE models are complete crap!" the woman said.

"But Miss Grandis, we just have to try again." Sanson tried to calm her down.

"Try again? The client is going to come to us personally in one week!" Grandis started to cry.

"I have to agree with Sanson. We should just follow their tracks." Hanson said to Grandis.

"That's a good idea." Grandis said. "And we'll mug her for it. Also, we'll teach that kid a lesson in respect."

'I always thought they were brainless.' Shinji heard the conversation. "We need to leave. Now." he warned the others.

"I know a place you can stay." Jean told them. "My uncle lives on the outskirts of Paris-5. He hasn't had any visitors in a while."

"I just hope he's not too friendly. With those guys chasing us, they may find us soon." Keiichi told him.

"He knows when certain people are trouble." Jean assured him.

* * *

 _Outskirts of Paris-5_

"Why did you come here anyway?" Keiichi asked Shinji.

"I just happen to be in the neighborhood and decided to visit. It was, Johan here, who told me where you were." Shinji explained.

"It's Jean." Nadia corrected. "In any case, It's good to see you."

"Likewise." Shinji said. "Who were those guys anyway?"

"They're called the Grandis Gang." Keiichi said. "I don't know what their deal is with us. But, they seem to be interested in the jewel in Nadia's necklace. They're usually the kind of thieves you would expect to steals from museums. Their car came up to a house. "Is this the place?" Keiichi asked.

"Yes." Jean said. "I'll introduce you to him."

Shinji yawned. "I hope he has spare beds."

"We have guest rooms. So, I think you can stay in one of them." Jean said. He then knocked on the door. "Hello."

The door opened for them to see a man, around Keiichi's age. "Jean, my boy. It's good to see you. Who are these guys?"

"Friends of mine. They're the latest victims of the Grandis Gang." Jean said.

"Them again?" his uncle asked. "They've been pretty active as of late. Well, any enemy of them is a friend of mine. Your welcome to stay here for a bit. Make yourself at home."

"Actually, if you don't mind, I feel like I'm about to pass out. Can you show me to the guest room?" Shinji asked.

"Sure. Also, there's some food in the fridge, if you want to eat something." he said as he walked to the room.

"Thank you." Shinji said to the man. He closed the door and crashed on the bed. 'What can I do? I don't want to have her hate me forever. But, I can't let my parents down. I'll have to talk to them, tomorrow.'

* * *

 _6 Hours Later_

Shinji woke up, got a can of soda, and walked outside, seeing the beauty of nature after spending most of his life in a city.

"It's beautiful, isn't it?" He heard a voice from behind him. A voice he knows too well.

"Yeah." Shinji said. "I kinda envy you. You get to see all this and I get to stay in grey buildings, which may as well be giant gravestones."

Nadia walked to him. "I heard from your parents that you are going to be a member of SEELE. Congrats."

"Thanks, I still have to do something for the General, but he is giving me time off until he figures out something." Shinji lied.

"That's sounds pretty nice of him. Usually a General wouldn't give a subordinate a day off immediately after getting in." Nadia said.

"The training was hell." Shinji convinced her. "I have to be in peak condition if he expects me to do whatever he wants me to do."

Nadia looked at him. "I hope you get to do that final task. Your parents are counting on you."

"Thank you." Shinji said to her as he yawned. He then saw a blue light in the sky. "I must really be pretty tired. I see a blue light coming from the sky."

Nadia saw the light as well. The light went to the ground, exploding. "What happened." a shocked Nadia asked.

"Go back to the house and tell everyone what happened." an equally shocked Shinji told her. He ran to the impact where there was a small town. People were screaming as a strange group of people who wore masks started attacking. "Holy Jesus." He helped a family. "What's happening? Who are these guys?" Shinji asked.

"I really don't know." the man said.

"You need to run, now!" Shinji told them. "I'll try to hold them off!"

"Thank you." the woman said.

Shinji ran up to one of the masked men, took his knife and sliced his neck. He then took the gun from him and shot every single masked man. He heard gun shots from behind him. "No." he whispered to himself seeing the dead family.

He got knocked out from the bud of a rifle. "Looks like this one wants to play hero." one man said.

"Let take him to Gargoyle. I'm sure he loves to know who would want to take out some of our men." another said.

Meanwhile with Nadia. She warned the others and asked for help. Keiichi, Jean, and his uncle joined her to the impact. They found a family laying on the ground. They were dead, all but one. A little girl, who was about five years old. Jean's uncle took her back to the house. They went to the town to find the place ruined and empty. "SHINJI!" Nadia yelled.

"SHINJI IKARI!" Keiichi yelled as well. But to no avail, no one answered back.

"Guys! I found something!" Jean found a dead soldier. A masked man, armed to the teeth. "This has to be one of the guys who attacked this place."

"Let's go back and call the authorities." Keiichi said.

"What about Shinji?" Nadia asked.

"He's a member of SEELE, right? Or he will be? I'm sure he can take care of himself." Keiichi assured him.

* * *

 _?_

"Wake up." Shinji was still knocked out from the blow to the head. One man slapped him. "Wake up." He said as Shinji started to snap out of it. "Our leader would like a word with you."

Shinji tried to break loose of the bindings, only to find out they were hand cuffs. "So, you must be the one who killed my men." says a man who looks like the leader. He wore a mask like everyone else, but wore red.

"After killing an entire town." Shinji responded. "And I'll kill them again."

"Color me impressed, though. I would never guess that a boy would kill one of my men, let alone a human." the leader said.

'Human? Jesus Christ. Who the hell are these guys.' a scared Shinji started to ask. "Who are you?"

The leader thought he might ask that. "My name is Gargoyle, leader of the Neo-Atlanteans. I'm sure you are now aware that you have officially join a war that you cannot possibly win."

Shinji was even more confused. "War? You mean there's someone else?"

"I already said to much." Gargoyle said. "I'll just cut to the chase. I'm looking for a jewel. A diamond shaped sapphire. Ever heard of it?"

'What the hell? How do they know about this. There's no way SEELE could forget about these guys.' Shinji was now scared out of his mind. 'Oh, Jesus Christ. I can't tell them. I have to refuse to tell them.' "If you kill me, a huge military organization will take you out."

Gargoyle laughed. "I'm sure you are aware of the position that your in. Even if you are speaking the truth, it wouldn't matter. We have more men and weapons than anything mere humans have. I will say it one more time. Where's the Blue Water?"

'I'm sorry, but if you were in my position, you would have done the same thing.' he thought to himself. "I never heard of anything ridiculous in my entire life."

"A real shame, but not unexpected." Gargoyle said with a calm tone. "I was told you are an kid hero made true and even with fear overwhelming you, you didn't back down. If you weren't a human, I'd have you join me. But, unfortunately... Lock him in the prison." He ordered one of the soldiers. "We'll have this talk again, buddy."

"You monster." Shinji yelled at him.

"Thanks, I'll call you when I need you." Gargoyle hand-waved the insult.

'Dammit! I'm sorry, Mother. I'm sorry, Father. I failed.' Shinji thought in despair.

* * *

 _AN: Shinji was captured by a mysterious force. What happens next? Find out in the next chapter._


	3. Favorable Company

_Disclaimer: Evangelion and Secret of Blue Water belong to Gainax. Paranoia Agent belongs to Madhouse._

* * *

 **Traitors of the Stars: Genesis**

 **Chapter 3: Favorable Company**

 _?_

Shinji was in a cell, sitting on a bed wallowing in despair. 'Why am I here? They could have killed me, but they let me live. Why would they?'

A door opened. "It's your lucky day, kid. You got some roommates." A man took two men to the other cell while the other threw a women with Shinji. Shinji recognized them immediately.

"So the master thieves have finally met their match?" Shinji said smiling, but with his head still down.

"You're that brat! You never intended to keep your end of the bargain didn't you?" Grandis asked.

"Does it really matter, now." Shinji said. "We are captured by a unknown cult-like army in the middle of who knows where. No one is going to save us. No one in their right minds would save a bunch of thieves and I don't know who would bother to save me."

Grandis was dumbfounded. "I can't believe this. This is the boy who tried to betray us? Acting like this only when things go the opposite direction. What happened to the daring adventurer, kicking ass and taking names?"

"Just leave him, miss. If he wants to die in this hellhole, let him." The man named Hanson told her.

Grandis looked at Shinji. "And to think I had some amount of respect for you." She said in a disappointing manner. They then heard explosions not far from where they were. "Looks like you were wrong. Someone is here!"

"But are they here to save us?" Shinji asked.

A soldier busted the door down, but it wasn't like the soldier that threw them in there. "We have prisoners here!" One of them said.

"Then save them! The Emperor made this a rescue mission didn't he?" A commander ordered them.

"Stand back." The soldiers told them. They did so when they put what looked like foam in the locks. The lock exploded and they escaped from the cell. Shinji attempted to stay, but a soldier grabbed him. "We need to go now!"

Shinji stood up, fearing what would happen if he didn't. "We have an safe transport! Make your way there and get them out of there!"

"Understood." They moved through the base with the masked men fighting off against the soldiers who saved them.

They made their way to the dock and found a submarine. 'It's either enter the sub and live to fight another day or go back to the cell and die. Nothing ventured, nothing gained.' Shinji thought to himself.

* * *

 _Outskirts of Paris-5, Jean's House_

"I told them everything we know." Keiichi said to Nadia and Jean.

"I'm still a little unsure of that masked man. Who is he and what is he a part of?" Jean asked.

"They're a group of soldiers headed by a man named Gargoyle." They heard a voice from the front door. "The door was open."

"Who are you?" Keiichi asked in a threatening tone.

"Oh, I see you met Electra." Jean's uncle came to the room. "She came as soon as I got back. I forgot to mention her, I was busy with the little girl."

"How is she, exactly?" Nadia asked.

"She's fine physically, but she seems to be in shock." He said to her. "Guess I shouldn't be surprised, after all that." He then noticed something different. "Where's Shinji, by the way?"

"Gone." Electra said. "Gargoyle's men have him captured somewhere. I fled the scene before I got caught. Like him, I did what I could to save everyone."

"Who are you, exactly?" Keiichi asked.

"Just a member of the Saviors of Humanity." She told them. "I can help you find this Shinji. But you must come with me. Knowing Gargoyle, he'll probably take him to turn into a slave at best or a savage at worst. If it is the latter, he might snap out of it if he saw a familiar face."

Keiichi stepped in. "I'll go. Nadia, you stay here."

"No. Shinji need's help." Nadia also stepped forward. "I want to help him."

"I'll also go." Jean said. "Shinji is my friend. I would move Heaven and Earth to save him from Hell."

"Alright then, let's go." Electra said. "We have a special kind of transportation. I hope you don't mind going up north."

"Can you take care of the girl?" Jean asked his uncle.

"Of course. Just be careful." Jean's uncle said to him before he left. "Now then." He opened the door to find the bed empty and the window open. "Wait!" But they were already gone. "Great."

After travelling a long way in Keiichi's car, they made their way north. "This way." She pointed to the beach.

When they made it, a huge submarine came up from the ocean. "What the..." Keiichi was awestruck.

Everyone else had the same reaction. "Ladies and Gentlemen, behold the Nautilus." Electra said.

"What an amazing vessel! I have never seen anything like this before!" Jean said excitedly. "Sure, SEELE has some impressive stuff, but this thing dwarfs their submarines!"

"The Captain might be willing to meet with you. If I told him the gravity of your circumstance, he could help you with rescuing Shinji." Electra offered.

"Alright. Let's not keep him waiting then." Nadia said coming aboard the Nautilus.

"Hang on." Jean said. "Let me get my bag."

He opened the trunk. "Hello." A voice scared Jean as he saw the girl.

"What are you doing here?" Jean asked.

"I wanted to join you." The girl said.

"For what reason?" Electra asked.

"I wanted to let Shinji know that I'm sorry." The girls cheerful demeanor turned into sorrow. "It's kinda my fault that he got captured my those masked men."

"What is your name?" Electra asked.

"Marie." the girl said.

"Well then, Marie. Welcome aboard." Electra said to the dismay of everyone else.

"This is a child your bringing with us." Keiichi told her. "She's ten years younger then these two."

"We have safe rooms and, besides, this is the most advanced submarine we have. It's going to take a lot of missiles to take us out." Electra assured everyone.

"What about my parents?" Marie asked.

Everyone was shocked. "I'm sorry." Nadia said.

"No. They have to be alive, they have to." Marie started to cry.

"Look, I'm sorry this happened." Nadia hugged her. "I really am."

* * *

 _Thunder Child_ _, English Channel_

"Those guys were insane. I'm sure these guys are better at keeping guests." Sanson said.

"I just hope that he snaps out of it." Hanson said pointing at Shinji.

"Hey, listen." Grandis said. "I will not stand idly by and let you beat yourself up. Now tell me why are you acting like this."

"I failed." Shinji said. "I failed to protect them. An entire family killed and for what?" Shinji started breaking down in tears. "That little girl looked no more than five years old. I failed them and by extant I failed my parents."

Grandis and her henchmen were shocked upon hearing this. "I'm sorry, I didn't know." She said to him.

Shinji, still crying, collapsed in the bed. "How can I save people, if I can't even protect an entire family?"

Grandis pulled him up and gave him a hug. "I'm sorry and, for what it's worth, I wished it would have ended differently. But it's pasted. Just hope they're in a better place. You can either have this event run your life or you can use it to strengthen your resolve."

Shinji hugged her back. 'Strengthen my resolve? is that really possible?' "Thank you. Grandis." he said. "I feel a little better, now."

"Remember, if you want to tell me anything, I'm all ears." Grandis told him.

"Shinji Ikari." He said.

"I'm sorry." She asked confusingly.

"I never did tell you my name, did I?" Shinji asked. "It's Shinji Ikari."

"Alright then, Shinji." Grandis said. "I'm sure you have some questions."

"Just one, actually." Shinji said. "Why steal the jewel on the necklace?"

"We meet a man named Gargoyle. I'm sure you and him already meet each other? He told us if we can get it, he will pay us, handsomely." Grandis reveled. "What I didn't expect was that he would betray us the way he did."

The door open to see a man in robes entering. "You there. Shinji Ikari."

Shinji stood up. "Yes?"

"The Emperor would like to see you." He said as Shinji followed him.

After a long walk, they finally made it to the bridge, where the Emperor was waiting. The man bowed "My lord. I brought the boy as you asked."

The emperor was shrouded in darkness and the only thing that was visible was his hand petting a white lion. "I thank you, Pericles." Said a kind voice. "Now, Shinji Ikari. I would like to talk." He said to Shinji, but noticed he was scared. "Don't worry, I'm not like Gargoyle. Here, I'll even let you pet Bast." He offered him. Shinji tried to pet her, but the lion swiped his hand, causing him to step back. "Don't worry, after a while you'll grow on her." He said. "In any case, welcome aboard to the Thunder Child. I am Emperor Neo Icon Epiphanes, of course you can call me Emperor Neo or just Neo, if you want to be friendly."

"I have questions, Emperor Neo. If you don't mind. Who are you guys? What's going on? Who were those Neo-Atlanteans people? And what does this "Blue Water" have to do with anything." Shinji asked.

"Long story short. We are Atlanteans, but don't get the wrong idea. Like I said, we are nothing like them." Neo explained. "We are in a war with the Neo-Atlanteans, who are also Atlanteans, they just hate the way things run. As for the Blue Water, I'm not entirely sure, but they want it, so that's enough of a reason to keep it from him. The only problem is I don't know where it is. I don't suppose you know where it is?"

"I've seen a lot of sapphires, but I don't think they have any relation with it." Shinji said.

"Lying is not your strong suit. If you want me to let you go, I need information. A fair deal don't you think, freedom for information?" Neo said.

Shinji sighed. "It's on a necklace. A girl is wearing it right now. Could be anywhere."

"Thank you, Shinji. Every little bit helps." He said. "Pericles, please escort our guest back into his room and send him and his fellows some of our finest food for him to eat."

"At once, my lord." Pericles bowed again.

"You have a good heart, Shinji Ikari." Neo said. "I would hate to see it ripped out."

'That's not animus at all.' Shinji thought to himself.

"Let's go, kid." Pericles said to him.

After reaching the rooms and waiting for the food to come. Shinji and the Grandis Gang talked about leaving Nadia alone, which they agreed since there was no real reason to get it anymore. "Thank you. I really appropriate that."

"Don't mention it. Even if we did have a reason, I wouldn't anyway." Grandis told him. "Especially with you involved. Taking on those soldiers all by yourself is pretty ballsy."

"I do have my moments." Shinji boasted.

The door opened. "Ladies and gentlemen. Dinner is served." Pericles said bringing the food in.

They saw that the food was strange looking, it was a group of bizarre-looking squids and worms. Everything else looked okay, apple cabbage stew and sweet rolls. They saw the main course, a huge boar, cooked to perfection. Shinji tried a bite of a worm and, to everyone's shock, he enjoyed it. "Are you going to have those?" He asked the Grandis Gang who gave him the rest of the squids and worms.

"He must have an iron stomach." Hanson said.

"No kidding. I'll eat anything, but he's just eating those things like he's eaten them before." Sanson said.

"Thanks for the food." Shinji said to Pericles.

"I'm glad that you enjoy it." He said. "I'll see myself out."

"Oh, Pericles, was it?" Shinji got his attention. "I would like to join you in attacking the Neo-Atlanteans."

Pericles and the Grandis Gang were surprised at the sudden request. "Are you absolutely sure?"

"This Gargoyle made this personal. They killed an entire village for who knows what reason and captured and would have tortured me if you guys didn't come." Shinji said. "Let me help you as you helped me."

"I'll let the Emperor know this." Pericles said. "I will be back with an answer." Pericles left the room and the Grandis Gang looked at him, shocked.

"I hope you know what you're doing." Grandis said.

"I'll be fine. If you want to leave, then go straight ahead. I'm going to fight, wipe them from the earth." Shinji said with determination in his eyes.

* * *

 _Nautilus, Straight of Dover_

"I informed the Captain of our little stowaway and he decided to keep her here." Electra said. "Now in order to rescue Shinji and whoever the Neo-Atlanteans took, we have to look for the base. Luckily for us we know where the base is, but we don't know the layout, so rescuing them might be a little difficult."

"You can still save him right?" Nadia asked.

"Of course. We give you our word." Electra said.

An intercom turned on. "Electra come to the Bridge. I repeat. Electra come to the Bridge."

"Looks like the Captain needs me." Electra said. "I'll be back."

Electra came to the bridge. "Electra. We have a problem." says the Captain.

"What is it, sir?" She asked.

He pointed to the screen. "Someone already came here." pointing at the destroyed base.

"Was it who I think it was?" Electra asked.

"Only one person can truly cause this massive destruction." the Captain said. "Emperor Neo."

* * *

 _AN: Looks like war is in the horizon and Shinji got swept up in it and the Nautilus is not to far behind. What happens next? Find out in the next chapter._


	4. The White Whale

_Disclaimer: Evangelion and Secret of the Blue Water belongs to Gainax. Paranoia Agent belongs to Madhouse._

* * *

 **Traitors of the Star: Genesis**

 **Chapter 4: The White Whale**

 _Nautilus_

"If he came here, then the boy must be in one of his subs." Electra suspected.

"I can only hope so." Nemo said. "Neo was always more interested in enacting revenge against Gargoyle than rescuing prisoners."

"What should we tell our guests?" She asked.

"Tell them... We're going somewhere cold. We need guidance and only he can help us there." Nemo said. "If they asked about this 'Shinji Ikari', then say he is somewhere safe."

"Understood." Electra said as she left.

'I really hope we can work together, Emperor Neo.' Nemo contemplated. 'Humanity is counting on us.'

Back in the guest rooms, the group were asking talking about Shinji. "If these guys can save him. We will be in their debt." Keiichi said.

"Are you sure?" Jean asked. "I, personally, don't like being in debt to one person for too long."

"It's a figure of speech, Jean." Keiichi said. "I just hope they pull it off."

"We don't need to." They heard Electra from the doorway. "Someone already beat us to it. Don't worry, this someone is an ally. Shinji's safe."

"Who is this 'someone'?" Nadia asked.

"If you must know, his name is Emperor Neo Icon Epiphanes." Electra said. "I know, name's a mouthful. If Shinji is with him, then he should be safe."

"Then we can go straight home, right?" Jean said.

Electra sighed. "I wish it was that easy. Even though we are on good terms, we stay out of each others way. He let's us rescue prisoners, and we let him destroy bases. He has a large army at his beck and call and we are just one crew. Yes a good crew in a good sub, but we are still one. Only he has a army big enough to take Gargoyle's on."

"So, what now? Do we just wait and hope that they are willing enough to listen?" Keiichi said.

"We are meeting an old friend of the captain and he would appreciate you coming with him." she said. "The only catch is your going to have to wear winter clothes. We are going somewhere cold." Electra started to leave. "I'll send someone to get your clothes ready."

"I hate the cold." Marie said.

"You don't have to go if you don't want to." Electra said. "But one of you are going to have to stay here with her until we get back."

"I'll stay." Keiichi said. "I'll trust you with these two."

"Are you sure, daddy?" Nadia said.

"Of course, I see no reason 'not' to trust them." He told her.

"Then it's decided. You two will come with us while he watches the girl." Electra left. 'Daddy? She really doesn't know who she really is?'

* * *

 _Thunder Child_

"My Lord, we are approaching the palace." Pericles said.

"Good. Get our guests. If they want to join us, we should show him what we are fighting for." Neo said, petting Bast.

"Yes sir." Pericles said.

Back in the rooms Shinji was playing cards with Grandis while Hanson and Sanson played old school games on their handheld. "You are pretty good at this, Shinji." Grandis said.

"You can thank my father. He showed me the ropes on how to pick the right cards to play at the right time." Shinji boasted.

"Well, he definitely taught you well." Grandis said, impressed by his skill in poker.

Pericles entered the room. "The Emperor wishes to invite you to his city."

"Alright. I really would like to see this secret city." Shinji said. "Are you coming?" He asked the others.

"Are you sure?" Grandis said.

Pericles smiled. "The more the merrier."

"C'mon boys! Let's check this city out!" Said Grandis to her gang.

"Yes, ma'am!" Hanson and Sanson said.

"Follow me." Pericles said.

After reaching the bridge, they were met with the shadow figure of the Emperor next to his pet white lion. "I am honored that you would fight for us, even though you are not one of us." Neo said.

"He made it personal." Shinji said. "Not to mention he kill a good number of civilians."

"Don't let rage consume you, Ikari." Said Neo as he got up from his captain's chair, revealing something that was more of a machine than that of a man. "It consumed me once."

Shinji was shocked. 'What the hell is this? This is not real.'

Neo saw Shinji and the others shocked. "Don't worry. I may look like a machine, but deep inside, I am still a man."

Shinji was trying to comprehend. "How did..."

"It was something that happened a long time ago. I just kinda got used to it." Neo told Shinji. "Maybe, if your interested, I can tell you that story. But, now is not the time for story telling, we have a feast to prepare. Onward to Agharta!"

* * *

 _Antartica_

"This is where his 'friend' is?" Jean asked Electra.

"He likes his seclusion. And where better can he live in peace than in Antartica." Electra said.

"He's also the main reason that we are still around, believe it or not." said the Captain as he started to leave the Nautilus. "Saved our lives before, we are indebted to him."

"I take it your the captain?" Jean asked.

"Yes. I am Captain Nemo." he said.

"It's an honor to finally meet you." Nadia said to him.

"I thank you." He said back. "We must go."

They traveled inside a cave until they found a huge underground paradise with a red light shining upon them. "I have never seen anything like this. This looks beautiful." Nadia said.

"Yes, you do." Jean said accidentally.

"Huh?" Nadia said hearing Jean's slip.

"Yes, it does." Jean tried to cover what he said up, but it was in vain.

"Right." But Nadia played along. Nemo and Electra also heard him but pretended to not hear him.

They then appeared in another part of the cave with the normal light and a pool large enough to fit an entire city block with an island with a huge tree in the middle of it. "This is the place." Electra told them. "Let the Captain handle this."

"Iilon!" Nemo said loudly. "Please, listen to my pleas. We require your advise."

They here a rumble. "I was expecting you, old friend."

A giant white whale came from the pool. "Whoa." Nadia and Jean said.

"I am Iilon, the keeper of knowledge and guardian of the Tree of Life." the whale said. "To what do I owe this visit?"

"I am looking for a boy. That boys name is Shinji Ikari." Nemo said. "He was captured by Gargoyle after attempting to save a village."

"That is grim news indeed. What do you think became of him?" Iilon asked.

"Emperor Neo rescued him, which is unusual considering he would rather bomb a Neo-Atlantean base than do any rescue missions." Nemo explained. "I wish to know what has become of this Shinji Ikari."

The whale focused on looking for Shinji, and in a minute he found him. "Shinji is indeed safe. He is in the ancient city of Agharta, where Emperor Neo resides. He volunteered to fight by their side." Iilon said to everyone's shock. "I assume you are going to get him out of this?"

"No." Nemo said. "If he volunteered, then he has made his choice. It's a better alternative than what Gargoyle could do to him."

"Understood. I hope your judgement is well placed." Everyone started to leave. "Wait." Iilon said. "I wish to speak with the girl."

Nadia was shocked to hear that the giant whale wants to talk to her, specifically. She walked up to him. "My name is Nadia."

"I know who you are." Iilon said. "I wish to show you something. It is a possibility, but it will happen if you don't do anything about it."

Iilon telepathically showed her a vision. In that vision, she was in the Antarctic with a dead creature in the pool, she turned around and saw Shinji Ikari. She ran up to him and gave him a hug. Shinji then stabbed her in the heart, she was shocked to see the dagger pierced her. She then looked up at him, he had red snake eyes and a serpentine tongue, and was smiling. He walked to the Tree of Life and burned it. She then saw a black void come from the tree. It took Shinji and, in a minute later, Nadia herself.

The vision suddenly stopped. "What is this? What does it mean?"

"It is something I hope will never come to pass. But if it does, you have to prevent it from happening." Iilon said. "If you are finished here, then you can leave."

Nadia was confused at what she saw. 'Why did he show me that? What connection does Shinji have with it?'

Jean noticed it. "Are you alright? What did you see?"

"A dying ember becoming a volcano." Nadia said cryptically.

Jean was uneasy. "I'll take that." getting the hint that she doesn't was to say more.

* * *

 _Agharta Palace_

Shinji saw an underground city, what they call 'Agharta', from the palace. "Looks like a grand city doesn't it?" Neo asked.

"I never seen an underground city before. An underground grove, maybe, but never a city." Shinji said in excitement.

"You should have seen what it looked like before we found it." Neo said. "It was a ruin, literally."

"You mean, you didn't make the city?" Shinji asked.

"No." Neo said. "In fact, we found this place a few years ago."

"This is amazing." Shinji said.

"Let's get down to business." Neo said. "We are fighting against the Neo-Atlanteans. You remember them, of course. You can back out though."

"No." Shinji said. "If left alone, they could bring destruction. I want to make sure they are gone."

"As you wish." Neo said. "I will also ask our other guests, maybe as technical. I really don't see them as a fighting force."

"I thank you, Emperor." Shinji said.

"I should thank you, Shinji Ikari." Neo said. "These Neo-Atlanteans don't know about the resolve of humans. Let's prove them wrong."

"Understood." Shinji smirked.

* * *

 _SEELE HQ, Tokyo-3_

"It's been a whole month since he was sent out, and not one word from him." Keel Lorenz said to Fuyutsuki.

"I know, but remember that it took me a while before I finally found what I was looking for?" Fuyutsuki tried to calm him down.

"Yes, but at least you gave updates. We don't even know if he's even in the city we sent him in." Lorenz said.

"Sir!" A SEELE member entered the room. "Shinji Ikari was captured by a group of men! It looked like armies at war!"

"That would explain why we haven't heard from him." Fuyutsuki joked.

"I hope you're not joking." Lorenz threatened.

"I'm not, sir!" He showed pictures. "This is Shinji being dragged away by masked men and this is the prison he was in while we were in stealth mode."

"Why did it take so long for you to come here?" Lorenz asked.

"We had to lay low, sir. First person that tried to fly out got blown up." The SEELE Member said.

"This is not a good sign." Lorenz thought long and hard. "Get Ryoji Kaji. I want him on this immediately."

"Are you sure? I mean he can be unpredictable and could cause collateral damage." Fuyutsuki said.

Lorenz looked at him and snarled. "He views Shinji as the younger brother he never had. Not to mention, we need people like him."

"I understand." Fuyutsuki said. "I'll tell him myself." he also said as he left.

* * *

 _Kaji's room, Tokyo-3_

Kaji was checking his guns. "Everything looks to be in order." He heard a knock. "Come in." He saw Fuyutsuki come in his room. "What do you want now? Infiltration?" he said

"Sadly, no." Fuyutsuki said. "Rescue mission."

"If your employees are so important to you, you tell your people go get them." Kaji said.

"There's two problems with that." Fuyutsuki said. "You are one of the best members SEELE ever had, number one. And two, the person you're rescuing is Shinji Ikari."

Kaji was shocked. 'Shinji Ikari captured. No.' "You really know how to push my buttons. How do you know it's Shinji."

"Is this picture not good enough." Fuyutsuki said as he showed the picture with an unconscious Shinji Ikari being dragged by masked men. "If this doesn't allow you do budge, nothing will."

Kaji looked at the picture and then at Fuyutsuki. "Tell me where to start and I'll handle the rest."

* * *

 _Kaji's been hired by SEELE to have a rescue mission. Will he be able to know the truth before it's to late? Find out next time._


	5. Reunion

_Disclaimer: Evangelioin and Secret of Blue Water belong to Gainax. Paranoia Agent belong to Madhouse._

* * *

 **Traitors of the Stars: Genesis**

 **Chapter 5: Reunion**

 _Agharta Palace_

"The Neo-Atlanteans are one of the most powerful forces we fought against." Neo said. "I hope you would fight until it is over."

"Of course. These 'men' are killing machines. Someone has to take them out." Shinji said.

"Let me tell you something." Neo said. "I have a father and sister. Had a mother, but she died. The last time I saw them was ten years ago, I was captured by the Neo-Atlanteans, imprisoned for seven years, and they tried indoctrinating me for four of those years. They even tried turning me into a machine, which he kind of succeeded. The only thing thing that's even remotely human anymore is everything save my limbs and as for my exoskeleton, an Atlantean rescue party found me and 'finished' the operation to save my life." Shinji was shocked discovering this. "It was in that moment I had to take them out, but we needed to keep them out of the surface. As you know, it had mixed results."

"What about this Gargoyle? Who is he, exactly?" Shinji asked.

Neo laughed. "Believe it or not, that's not his real name. It's Nemesis La Algol. I know, real original name right?"

Shinji laughed at the generic sounding name. "Little wonder he changed his name. But why Gargoyle?"

"I really don't know. Maybe he looked through the various monsters that humans believed in and thought the gargoyle was the only one people could take seriously. Anyway, he was the last emperor's adviser." Neo explained. "He really hated the humans. I don't really know why, but it might have something to do with oil spills and killing endangered animals for fun. My father tried to explain to him that there's others who are not like that, but one thing lead to another and, you know the rest."

"So he's a nutcase and a racist. Got it." Shinji said. "One last thing. Who are the Atlanteans? I thought they all died when Atlantis sunk."

"That was not us." Neo said. "It was a group of humans who were in the wrong place in the wrong time. I don't want to freak you out or anything, but... we're aliens." Shinji's eyes grew wide with surprise. "I know. Always the last place you look, right? It was many eons ago, we escaped from a group of invaders and we came here, hoping to start our civilization over again in peace. We were capable of building cities underwater and, not only that, we lived in them, because no one would find us."

"And this is the first time your interacting with humans?" Shinji asked.

Neo smirked. "In more ways than one."

* * *

 _Nautilus_

"So why would he do this if he doesn't know anything about humans?" Nadia asked.

"That's all he needs to know about them." Nemo told her. "We are not meant to be involved in human activity."

"So, Gargoyle thinks he is doing a good thing, but in our expense?" Keiichi asked.

"Yes and no. He want's to make the world safe for the wildlife. Killing humans is just an option." Says Nemo. "He's a nightmare, a living boogieman."

"That monster!" Nadia was angry. "Shinji is a part of this now. I wished we weren't a part of this."

"We all wish we weren't a part of this. I wanted to avoid surface contact as much as possible." Nemo said. "I'm sorry he had to be caught in the middle."

"Then why get us." Nadia asked.

"He knows you." Nemo told her. "I don't think he's going to take our word that we'd just take him back to you."

"He does have a point." Keiichi said. "I wouldn't want to take their word for it, either."

Nadia contemplated. 'If Shinji wants to fight against the Neo-Atlanteans, he's doing it for everyone, not just the humans, but the remaining Atlanteans that the Emperor's keeping safe as well. How can I call myself his equal if I deny him this.' "Can you contact the Emperor and let me see Shinji?" She asked.

"I maybe able to contact him. If he's in a good mood, he will welcome us in his city." Nemo said.

"I will take them back to their room." Electra offered.

"Don't worry. If things go smoothly, he can help us." Nemo assured everyone. "It's probably going to take a while to get there anyway."

* * *

 _Agharta Palace, Guest Bedroom_

"I can't believe that they're giving Shinji proper service, just because he offered to help their war efforts." Grandis was angry.

"Now, Miss Grandis, let's calm down here." Sanson said.

"Yes. We can just leave if we just play nice." Hanson tried to assure her.

Grandis calmed down. "Yes, you're right if things go smoothly we can go to the surface and go back to the way things were."

"Before you leave, I have a question to ask you?" a voice came from the window. "Where's Shinji?"

"Who are you?" Grandis asked.

"I'm your worst nightmare if you don't give me exactly what I need." the man said.

"Is that a threat?" Grandis asked. "Let me show you how whandle threats."

Hanson attacked him with two stun guns. It shocked the man, but it proved useless. He grabbed the stun guns and broke them. "Thanks. I needed some energizing." He then punched Hanson out.

Then Sanson caught him in a bear-hug. "Gotcha!" Sanson squeezed him as hard as he can, before getting kicked in the balls.

The man smiled. "Normally, I'd be pissed. But lucky you that was the best massage I got in forever." He then looked at Grandis. "Now, tell me where Shinji is and please don't make me ask a third time."

Grandis was scared. "He's in the throne room."

The man walked out of the room. "Thanks." he said leaving a shocked Grandis, a knocked-out Hanson, and a writhing in pain Sanson.

* * *

 _Agharta Palace, Throne Room_

Neo and Shinji were looking at the city in the balcony. "Are you ready to meet them?" Neo asked.

"It has been a while." Shinji said. "So what is it with you and Nemo anyway? You fight the same guy, yet you barely talk to each other."

Neo shrugged. "It's an ideal difference. He wants to stop the Neo-Atlanteans, but only if the humans are involved. I want to start a full scale war, I don't want them involved in our affairs for their protection. No offense, but I think it's bad enough for you to be a part of this."

"So that's it?" Shinji asked. "You're doing it for our benefit?"

"Short term answer. Yes." Neo confirmed. He heard a footsteps. He turned around an saw no-one. "Hide." He told Shinji. He walked into the throne room. "Show yourself!"

The man revealed himself. "I was hoping to find the King and, judging by your attire, I say you're the one. There maybe a god after all."

"I don't know who you are, but I assure you I mean you no harm." Neo tried to calm him down.

"I'm afraid that's not for you to decide." He said as he draws a gun on him. "Now where is he?"

"I don't know who your referring to." Neo said.

"Don't play dumb." Said the man. "Where is he?"

Then, Shinji came out of nowhere and tackled him. He then punched the man repeatedly, but he was overpowered and was pushed off of the man. Shinji then tried using knife tricks against him, only for his opponent to use similar knife tricks. They engaged in a knife fight, but shortly after it started, the man disarmed Shinji. Shinji then rammed into him, making him drop the knife, grabbed it, and held it to the man's throat.

The dark room was then illuminated by the emperor. Shinji was shocked to see who it was he was fighting. "Mr. Kaji?"

"Shinji?" He calmly said in response. "Looks like you made it out."

"What are you talking about?" Shinji was confused. "How did you find this place?"

"It wasn't to hard. Someone dropped a map." Kaji said, jokingly.

"You know this assassin?" Neo asked.

"Kaji is no assassin. He was one of my trainers." Shinji told him.

"Wait. What's going on here?" Kaji was just as confused as Shinji was. "I got called in by SEELE to rescue you and here you are, acting like good friends with the man." This shocked Shinji.

"SEELE sent you?" Shinji asked. "What do they know? What else do they know?"

"All they said was that you were captured and showed me a picture of the place you were sent to." Kaji said. "That's all they told me, I swear."

Shinji sighed calmly. "That's good. I would like to ask you a favor. If they call, make something up." He asked Kaji. "The last thing these people need is another army to fight. Can you please do that?"

"No problem." Kaji said, lifting Shinji's spirits. "You're parents are rooting for you by the way."

"How are they?" Shinji asked.

"They're fine. They don't know anything about this, so don't you worry." Kaji looked at the Emperor. "No hard feelings, right?"

"That remains to be seen." Neo said in an angry-sounding voice. "You live only because Shinji vouches for you. But pull something like that again, and it'll be more than just Shinji to save you."

"Understood." Kaji said. "Wouldn't have been the first time."

"Kaji can keep SEELE off your back. I know Gargoyle is a real threat to you, but Lorenz is a real nutjob, who knows what he could do if he finds out that you exist." Shinji said in defense of Kaji.

"For our sake, I hope your right." Neo said.

* * *

 _Agharta Docks: Thirty Minutes Later_

Emperor Neo, Shinji and Kaji were waiting for the Nautilus.

"So why is it called the Nautilus?" Shinji asked.

"I just you can say that Nemo is like me, in a sense." Neo told him. "He named his ship after the one in 20,000 Leagues Under the Sea. I named the Thunder Child from that one ship in War of the Worlds. Pretty ironic, I know. Technically, the Nautilus is bigger and stronger than the Thunder Child, but the Thunder Child has more sentimental value than anything else."

"Jules Verne and H. G. Wells." Kaji thought out-loud, he then figured it out. "You are fans of steam-punk stories."

"You got it. Good writers, I'm sure you would like their stories." Neo chuckled. "They should be here, any minute now."

Shinji felt rumbling from the ground. "Do you feel that?"

"They're coming." Neo said to Shinji.

A giant submarine came from the water. "Sweet Jesus." Kaji said silently. "This really isn't SEELE's work."

They see a group of people come from the submarine and came to the dock. "Finally able to see me face-to-face, Captain?" Emperor Neo said.

"Yes, I am, Emperor." The Captain said.

Shinji saw Nadia and walked towards her. "Hi Nadia."

Nadia noticed Shinji. "Shinji? You're really here?"

"I think so. I don't really know what's going on to be honest." Shinji joked.

Nadia pulled him to a hug. "Thank God you're safe."

"Shinji." Shinji heard a voice from behind Nadia.

He was shocked to see it was the little girl he tried to save. "You're not dead." He hugged the girl as tight as he could crying tears of joy that she was still alive. "Thank God! Thank you, God!"

* * *

 _Shinji and Nadia has been reunited. Will they work together to stop the Neo-Atlanteans? Or will Shinji remember his mission?_


	6. Going Home

_Disclaimer: Evangelion and Secret of the Blue Water is owned by Gainax. Paranoia Agent is owned by Madhouse._

* * *

 **Traitors of the Stars: Genesis**

 **Chapter 6: Going Home**

 _Agharta Palace Guest Rooms_

Shinji, Nadia, and Jean sat by table drinking juice. Marie is

"It's good to see all of you again." Shinji said tearfully.

"Same here. I thought you were lost forever until the captain came and told us what happened." Jean told him.

"There was more to it then that." Nadia said to Jean. "But there were alot of things that were complicated."

"I guess it doesn't matter now." He hugged them. "You're here." Shinji thought about the girl. "Did her parents survive?"

"You mean Marie?" Nadia asked. "No. I'm afraid not."

"Oh, I am sorry. I didn't know." Shinji apologized.

"Don't apologize. It wasn't your fault. It was the Neo-Atlanteans, they did it." Jean said.

"I tried to save them." Shinji whispered.

"You did what you had to." Nadia calmed him down.

"You're right, I can't do anything for them now." Shinji realized. "At the very least, we can try to care for Marie. Where's Uncle Keiichi?"

"Talking to that Kaji guy and the Grandis Gang." Nadia said. "I still can believe you talk them into coming with us."

"They're cool. Grandis is a nice woman once you get to know her and Hanson and Sanson are really nice guys. I always thought thieves were as bad as murderers." Shinji said. "Turns out you really get to know a person if you spend time with them in cell." He suddenly stood up. "I need to go out for a bit, I need some air."

"In an underground city?" Jean said.

"It's complicated, Jean." Shinji said. "It's still good to see you again."

Shinji started to leave. "He finally called me Jean." Jean said silently.

* * *

 _Agharta Throne Room_

Earlier that day, Neo and Nemo talked. "So, is Nadia safe?"

"Yes, I had to meet an old friend." Nemo said. "That's how I found you."

"It's good that you came to me." Neo sighed in relief. "She'll be safe here. The Neo-Atlanteans can't find us here. If they could, they would have taken the city out."

Nemo noticed his pet lion. "Has she been here long?"

"Who? Bast? Yes, a few years ago she joined us. Everywhere I go, she goes." Neo smiled.

"I didn't see her with you earlier." Nemo noted.

"Turns out she was pregnant. I thought it was time for her to get to know another lion like her." Neo thought. "Turns out she suceeded in producing a cub. A male cub."

"Has the great emperor thought of a name for him?" Nemo said.

Neo sighed. "That's the thing. I'm thinking of giving him to Nadia for a pet."

"Are you sure?" Nemo was shocked apon hearing this.

"Only when they're ready to part." Neo said. "I'll talk to Bast about it. Maybe if they met her, she will be more than happy to let him go with a nice person."

"That's very noble of you." Nemo patted him on the back.

"But I don't think they'll be ready to leave yet. Which pains me to ask." Neo turned to the Captain. "I would like to ask if Nadia stay with me. She will be safe and secure. Her father can stay too. At least until it's safe."

"I'll have to ask them." Nemo was deep in thought.

"You know as much as I do they're looking for her." Neo enforced. "Keep that in mind." He walked away.

He strolled around the halls until he heard the children talking to each other. "Did her parents survive?" He heard Shinji say.

"You mean Marie? No. I'm afraid not." He heard from Nadia.

'Marie, that's the child who were with them.' Neo thought.

"I'm sorry, I didn't know." Shinji said.

"Don't apologize." He heard from Jean. "It wasn't your fault. It was the Neo-Atlanteans, they did it."

Neo then heard Shinji say "I tried to save them."

"You did what you had to." After hearing Nadia say that it became clear.

'So that is you motivation.' Neo thought.

"You're right, I can't do anything for them now." He heard from Shinji.

"What am I doing." Neo whispered to himself as he walked away.

He started walking back the halls and bumped into Shinji. "I'm sure you're glad to catch up with them again. I would be spending more time with them."

"I really want to, but there's something's I need to think about." Shinji was lost in thought.

"Forgive me, but I happen to overhear part of the conversation you were having." the Emperor said. "There IS something you can do for the parents of that poor child."

"You think so?" Shinji asked.

"I know so." Neo replied. "You can get the bastards that did it. You still in?"

"You right." Shinji smiled. "It the only thing I can do for them. I still need to think about it."

"I hope you make the right decision." Neo said.

"I hope so too." Shinji looked at the Emperor.

* * *

 _Agharta Throne Room, The Next Day._

Nadia, Jean, Keiichi, and the Grandis Gang sat in a bench.

"Where's Shinji?" Jean asked.

"I don't know." Keiichi said to him. "I haven't seen him since we got here."

"Shinji stole the Blue Water!" They heard the guards say. "The Blue Water is gone." they were shocked to hear that.

"Shinji's no thief." Nadia said. "I know it in my heart that he is no thi..." She then noticed her necklace was missing. "What happened to my necklace?!"

The trio looked at the Grandis Gang. "Whoa! Don't put this on us." Grandis said sincerly.

"You can check everywhere on us, we don't have it." Hanson said.

"I hate to say it, but Shinji might actually took it, as well as this Blue Water they keep talking about." Sanson deduced.

"Shinji is not a thief!" Keiichi yelled.

"Then where is he?" Grandis asked. "And for that matter where's Kaji?"

* * *

 _Miles away from Tokyo-3_

Shinji and Kaji were riding in a V-TOL.

"That was a gutsy move back there." Kaji said.

"Even I didn't think that I would do it." Shinji congradulated himself.

"Well you did it, you found the Blue Water. You are definitely getting some special treatment from the people of SEELE." Kaji said. "Executive Lunches. Free days at the spa. Hell, they might even give you a huge promotion after this."

"I do feel bad about taking it though." Shinji frowned.

Kaji chuckled. "It's just jewelry to them, I don't think they know what they have. Just make up a story. In any case, your parents are going to be proud."

"I'm sure they're going to be surprised." Shinji frowned.

* * *

 _SEELE HQ, Heliport_

Shinji got off the V-TOL to see his parents. Yui opened her arms and Shinji ran and hug her. "Welcome home, Shinji."

Gendo patted him on the head. "I knew you could do it."

"Thanks." Shinji said. "I have some time to spare."

"Then let's go eat lunch. They have some udon available." Gendo said. "General Lorenz is out, so don't worry about arriving late."

"Thanks." Shinji walked with his parents to the Mess Hall. "What about Fuyutsuki?"

"I really don't know." Yui said. "But let's save the conversations for lunch."

* * *

 _SEELE HQ: Mess Hall_

The Ikari's were having udon while they were talking. "Sound's like a journey." Yui mentions. "But nothing an Ikari like you can't get out of."

"It was hardly a challenge." Shinji said. 'I can't let them know they're aliens, the media would be all over it. It's the least I can do for them after the stunt I pulled.'

Gendo finished his bowl. "Well, I hope Keiichi and Nadia are alright."

"Oh, yeah. I forgot to mention, Nadia has a boyfriend." Shinji announced.

"Really?" Gendo and Yui said in unison.

Yui chuckled. "I always knew she had it in her."

"Wait." Gendo said. "Who is he and what is he like?"

"His name is Jean." Shinji told his parents. "He's a pretty nice guy. Know's somethings about rockets."

"I'll take your word for it." Gendo said. "Anyways, they say that they sent Kaji over to help get you out. Not that he needed to of course."

"He gave me a fly back." Shinji said. "I couldn't have got out without him."

"Don't get me wrong. He always saw you as a younger brother." Gendo said. "But the problem is he worries too much."

They then heard an announcement. "SHINJI IKARI, PLEASE COME TO THE GENERAL'S OFFICE. I REPEAT, SHINJI IKARI, PLEASE COME TO THE GENERAL'S OFFICE."

Shinji started to leave. "You know what that means. Does either of you want the rest of the udon."

"I'll take it." Yui said.

"Shinji." Gendo stopped him for a moment. "I hope you impressed him. He's not an easy man to impress."

"Understood." Shinji left his parents.

* * *

 _SEELE HQ: General's Office._

Shinji went straight to the General's Office. "General Lorenz, sir."

Lorenz turned around. "It's good to see you again. I'd say you're late and should yell at you. But, given the circumstances, I'll lay off."

Shinji stood in attention. "Thank you, sir."

"I'm guessing you have the Sapphire." Lorenz reached out his hand.

"Yes, here it is." he gave it to him.

"I am proud of you. I usually don't send someone like you after something like this at your age, but I had convidence in you." Lorenz patted him on the back.

"Thank you, General Lorenz." Shinji was honored.

"And let it not be known that I am not a fair man." Keel Lorenz smirked. "How about we invade those people who kidnap you."

Shinji stood surprised. "How do you know about..."

"Come on, Shinji. I got people all over the place." Lorenz said sincerly. "Even that one town that these terrorist annihilated."

"So you can take them out?" Shinji asked.

"Yes, I can and I know where they are to top it all off." Lorenz showed a button. "I can make the announcement to take them out."

"They've taken everything away from them, even they're lives." Shinji smiled evily. "Do it."

"Okay. Take a load off." He said sincerly. "Tomorrow is a big day for you."

"Later." He left the office. He saw his parents waiting outside. "He said tomorrow is a big day for me."

"He always was the strange type." Gendo joked.

They heard Lorenz voice from the intercom. "EVERYONE PREPARE FOR BATTLE! WE HAVE SECURED A ROUTE TO AGHARTA!"

Shinji's eyes were wide with horror as he whispered, "No."

* * *

 _AN: Sorry for the LOOONG delay. I finally got out of my Metal Gear high. So expect some more chapters anytime soon._

 _SEELE has prepared a battle against the Atlantean Loyalist. Will Shinji stop the battle, or is the chain of command to great for him?_


	7. Despair

_Disclaimer: Evangelion and Secret of Blue Water belongs to Gainax. Paranoia Agent is owned by Madhouse._

* * *

 **Traitors of the Stars: Genesis**

 **Chapter 7: Despair**

 _SEELE HQ, General's Office_

Shinji burst into the Office. "LORENZ! YOU SAID YOU WOULD TAKE CARE OF THE PEOPLE WHO KIDNAPPED ME!"

Lorenz just sighed. "Isn't that what I said I was doing." He said calmly.

Shinji was more furious. "I WANT YOU TO CANCEL THE ORDER!"

"Okay, fine just let me push this button and..." Lorenz smashed the intercom. "Oh no. I 'accidentally' broke it. It's going to take a good while to get it up and running again."

"You're a monster." Shinji said shuttering.

"And so are these Atlanteans you seem to associate yourself with." Lorenz chuckled.

"What do you know about them?" Shinji felt defeated.

"I know enough. Known about them for a long time." Lorenz smiled. "To be honest, they all must die. I really needed this necklace. I didn't really need you that much. I could just get someone else to do it for me." Shinji looked at Lorenz in pure horror. "I just sent you to get it because the thought of a loving teenage girl having her prize possession stolen by someone who she considered family is really hilarious."

"I don't know why I even decided to follow you." Shinji was in a state of vengence. "I don't even know why anyone decided to follow you. Now I understand why Kaji left."

"That's why one of the slang words for follower is sheep." Lorenz joked. "Show them the way and they'll follow." Shinji pulled out a knife to threaten him. "What are you going to do with that? Kill me?" Shinji was hesitant. "If you kill me, you will be arrested and striped of your duties. But, I am a fair man. If you leave now, you may have a chance to save them."

Shinji put the knife back in his sheath. "You will regret this decision."

"Oh, trust me as soon as you come back. I'll be long gone." Lorenz laughed.

* * *

 _SEELE HQ, Mess Hall_

Kaji was looking at the menu. "I'll have some onigiri."

Shinji bursted into the Mess Hall. "Kaji. I need you to come with me."

Kaji was confused. "Okay, but where?"

Shinji looked at him and whispered. "We're going back."

"Why?" Kaji asked.

"General Lorenz ordered his army to wipe out the city." Shinji said desperately.

Kaji was in shock. "That bastard. Never did like him."

"The Neo-Atlanteans they can handle. SEELE is a top of the line military organization, there's now way they're going to win." Shinji pleaded. "Kaji please, I can't do this without you."

"Alright." Kaji accepted. "You don't have to tell me twice."

"Excuse me, sir." the man at the counter got Kaji's attention. "Your onigiri is here."

Kaji snatched it from his hand and said, "Thanks." and ran straight to the heliport with Shinji.

* * *

 _SEELE HQ, Heliport_

Shinji was stopped by his parents. "Whoa. Wait a minute what's the matter?" Gendo asked Shinji ran past them.

"Shinji, please tell us what's wrong." Yui pleaded.

Shinji took a deep, deep breath. "Nadia and Uncle Keiichi are in serious danger. That city that they said they were going to destroy? They're there." Shinji whispered.

"What?" Yui said.

Gendo was lost in thought. "Are you sure they're there?"

"Yes." Shinji said. "And it's not just them. There's innocent people there."

"I'm going to kill Lorenz." Yui said angrily.

"No! That's what they would expect from you." Shinji said. "Say that I relieved myself from my duties."

"Are you sure?" Gendo asked.

Shinji looked at them with hopeful eyes. "Yes. Just tell me when he leaves. He said he'll be gone by the time I get back. Just play along like you don't know what's happening."

"Alright." Gendo said.

"I don't like it, but if you say that it's for the best then I'll do it." Yui was hesitant.

Shinji tried comforting her. "It is. Thank you."

"Shinji we gotta go." Kaji shouted out.

"Alright! I'm coming!" Shinji shouted back. "I'll be back." Shinji went to the V-TOL that Kaji was piloting and waved to his parents, Gendo and Yui waved back. "We're going to need a sub." He told Kaji.

"I know a guy. My old college colleague, Ayerton. A real character, but when the chips are down he's willing to help." Kaji says as he lifts off.

* * *

 _London-6, Grenavan Mansion_

They walked down the halls of the mansion. "You didn't tell me that he was rich." Shinji said.

"Even I have my secrets." Kaji joked. "Listen. Like I said he may act eccentric, but he can help us."

"Alright. I hope you know what to do?" Shinji said.

"Don't worry." Kaji said smiling.

They opened the door to see a man slumped over the table with numerous beer bottles. "This is not what I was expecting."

Kaji sighed. "Only one way to wake him up."

He fill one of the cups with water and splashed it on him. The man was surprised. "Goddammit. Was having a perfect dream too." He looked at the direction where the water came from. "No. Way. Ryouji Kaji!"

"It's good to see you again, Ayerton." Kaji said with a smile before showing a frown. "That's what I want to say anyway."

"Why what happened." Ayerton was shocked that the happy go lucky guy they knew was frowning. "And who's this with you."

"We need one of your submarines. The fastest one you got." Kaji warned him. "I'll explain on the way."

"Alright. Your stunt woke me up completely, not that I was sleeping that long, so worry about any hangovers." Ayerton said to him.

They walked to the halls. "This is Shinji Ikari. The younger brother I always wanted." Kaji told Ayerton. "He is in desperate need of a sub."

"May I ask why?" Ayerton asked.

"I'm going to rescue or avenge a group of people." Shinji said coldly.

"If it's a rescue mission your going on, I know just the thing." Ayerton said with glee. They entered a room where they store submarines. There was a few subs in the water. Ayerton pointed to one of them. "This is the one you want. The Hattori. Named after the great Iga ninja, Hanzo. Relitivally small, but it's really fast and has a stealth mode. It can't show up on radar at all, though the only downside is you can't fool human eyes, unless the humans in question are complete morons."

"We'll take it." Shinji said.

"Good, he's ready when you are." Ayerton patted Shinji on the back.

Shinji and Kaji entered the sub. "We should get drink like old times." Kaji commented.

Ayerton laughed. "I wouldn't. Last time I did that, you challenged me to a drinking contest and lost."

Kaji chuckled. "Good point."

Kaji entered the sub. "Are you sure the SEELE army are not there yet?" Shinji asked.

"Trust me." Kaji said. "SEELE may act fast, but I can't say the same for they're battleships."

"Let's go to Agharta!" Shinji yelled.

* * *

 _The Hattori, Agharta Enterance_

Shinji saw the fleet of Neo-Atlanteans subs. "Damnit."

"These guys aren't SEELE. Who are they?" Kaji asked.

"Neo-Atlanteans. These guys are bad news. They want nothing more then to destroy humanity." Shinji warned him. "There was no way that they knew this was here. They must have followed SEELE from a safe distance."

"Great." Kaji sighed. "You know, I was hoping I wouldn't be part of a three-way battle."

"Don't worry. You know SEELE and you can tell the Neo-Atlanteans from the Loyalist from there masks." Shinji assured him. "Neo showed me a secret passage. It's in the ocean floor, goes straight to palace. I guess it's suppose to be some kind of escape route."

"Then let's go." Kaji said. They rode to the secret entrance.

* * *

 _Agharta Palace_

Shinji and Kaji exited the Hattori. Shinji was shocked at the state the city was in. There was fire in certain parts of the city and people were screaming in terror. "By the gods, what have I done."

"This isn't your fault. Remember, this is Keel Lorenz's fault." Kaji conforted him. "He's the one that did this. Now come on, they need your help."

They ran to the city proper to rescue the citizens from the Neo Atlanteans and the forces of SEELE. There were some Atlantean Loyalists sending them to a shelter. "Kaji, assist the soldiers with the citizens."

"You don't want help?" Kaji asked.

"If there's one thing I'm thankful for Lorenz, it's that he gave me one hell of a training session." Shinji smiled.

"Just don't let them kill you." Kaji said to him.

Shinji ran to the town. He saw some Neo-Atlantean and SEELE soldiers capturing citizens along the way, he killed them swiftly. "There's a shelter near the palace, go now!" he tells the citizens. He saw Neo-Atlanteans capture Keiichi, Nadia, Jean, everyone even the captain, Nemo, and right in front of them was the leader of the Neo-Atlanteans himself. "GARGOYLE!" Shinji ran to him and attempted to stab him, until a bullet pierced his gut. He looked at the direction of the the bullet that pierced him. It was the woman who was with the captain.

"SHINJI!" Nadia screamed.

"Good job, Electra." Gargoyle praised her, then turned to Shinji. "And you, I knew you'd be around. I just want you to know, no one gets away from me, I find them sooner or later."

"Bastard." Shinji coughed. "How did you find this place?"

"I just followed these human soldiers." Gargoyle admitted. "Funny. They keep saying it's for the best for humanity to seclude ourselves. I'm sick of it, sick of it all. So I figured I just kill humanity so we can live freely and comes humanity just to prove my point." He grabbed Shinji by the throat. "You are just digging you own graves." Shinji spat on his mask. "You know, you're just making it easier for me to kill you."

Gargoyle brutally beat Shinji to a pulp. "Enough! Please!" Nadia said as she got out of the grasp of the Neo-Atlanteans. "You made your point!"

Gargoyle stopped. "I really wish I can agree with you. But someone's got to die."

Gargoyle saw Shinji and pulled out a gun. "Wait!" Keiichi said. "I will die in his place."

Shinji was shocked. "Uncle Keiichi!? What are you doing!?"

"The right thing." Keiichi said.

"Father!? Please, there has to be another way." Nadia sobbed.

"This IS the only way!" Keiichi shouted. "Even if there was, what next?"

"I..." Nadia was at a lost for words.

"I admit this is a touching scene." Gargoyle pulled Shinji up. "Feels like I'm watching a movie. Shame though that I have to come in and ruin it."

He hands Shinji the gun. "What's this?"

"It's a gun, genius. Show your will to live." Gargoyle pointed to Keiichi. He didn't need to ask what he wants him to do next.

"Shinji, do it." Keiichi pleaded. "It's either me or you."

"Do it or it will be the both of you." Gargoyle threatened. "Clock. Is. Ticking."

'Bastard.' Shinji thought as he pointed the gun to his uncles head.

"If you have any last words to say to each other, say them now." Gargoyle offered.

Shinji started to cry. "Please. Please, forgive me." he said to Keiichi.

Keiichi smiled. "There's nothing to apologize for. I'm ready."

Shinji's hand was shaking and, in just one moment, fired. "NO!" Nadia screamed.

Gargoyle only sighed. "What the hell? I feel nothing at all." he turned to Shinji, who was shocked after what he did, and grabbed the gun. "Congratulations, you live another day." He punched him in the gut where the bullet was. Shinji was screaming with agony. "As a parting gift, I shall show you the face of the man who one this day."

Gargoyle slowly took of his mask to show Shinji and only Shinji the true face of Gargoyle. Shinji could not believe his eyes. "Master Fuyutsuki." Shinji whispered.

"Yes, now you know. The last hope for the Atlanteans was right under your nose the entire time." Fuyutsuki laughed before putting back on his mask. "Looks like you're passing out. Before you do that, tell me, where's the Blue Water."

"SEELE has it. If you want it, go get it." Shinji said as he started to lose consiousness.

Gargoyle sighed. "Damn it, Lorenz. Looks like you really have it in for us." He walked towards Nadia. "Let's go now, Princess. We don't have all day."

* * *

 _AN: Wow, talk about your dark ending to a chapter. War with SEELE and the Neo-Atlanteans has come. Keel Lorenz and Gargoyle, a.k.a. Nemesis La Algol, now shown to be Kozo Fuyutsuki. Two formidable leaders with a whole army at their beck and call. Shinji Ikari is the only one who can stop them now.  
_


	8. Saving Captain Nemo

_Disclaimer: Evangelion and Secret of Blue Water are owned by Studio Gainax. Paranoia Agent is owned by Studio Madhouse._

* * *

 **Traitors of the Stars: Genesis**

 **Chapter 8: Saving Captain Nemo**

 _Agharta Hospital_

Shinji was starting to wake up. "What happened?"

"You took a nasty spil near the docks." Kaji explained. "Took that bullet out from you. Something's strange though, if they wanted to kill you, they wouldn't aim at the gut."

"I remember those monsters taking them to..." Shinji realized something. "What happened to Uncle Keiichi!?"

Kaji was hesitant to tell him, but decided too anyway. "I'm afraid Keiichi didn't make it."

Shinji looked at his hands. "I did this. I did all of this."

"Gargoyle's the bad guy here." Kaji said. "Him and Keel Lorenz."

"I was the one who shot him!" Shinji said. "It was either him or both of us! Keiichi told me it's okay, but I don't..."

"I understand." Kaji confort him. "I understand the problem of taking a life against your will. I was hoping you wouldn't suffer the same fate. Wishful thinking on my part."

Shinji looked to Kaji. "You were forced to do that before?"

"Yes. It was then I decided to quit SEELE." Kaji said. "Nothing but friend killing. But, sorry for the change of subject, someone wants to see you."

Neo came from the shadows. "No, no, please no. I'm sorry!"

"Calm down Shinji." Neo said. "I'm not angry at you. But I do want answers. Why did you take her heirloom?"

"I didn't want to." Shinji pleaded. "But I can't tell you how many people died in SEELE just for failing a mission."

"Okay, who is SEELE?" Neo asked.

"A military organization runned by General Keel Lorenz." Shinji answered

"How did they find us?" Neo asked.

"I don't know." Shinji said. "He just said that he'd wipe out the Neo-Atlanteans in exchange for the sapphire."

"And they decided to attack us instead?" asked Neo.

"Yes. The Neo-Atlanteans must have followed them." Shinji said.

"I see." Neo was adding numbers in his head. "They killed my best friends. Bast and Pericles."

Shinji hung his head. "Gargoyle himself was a mole in SEELE."

Kaji was surprised. "Who was it."

"My master, Kozo Fuyutsuki." Shinji said.

"Then we have common enemies." Neo said. "That sapphire is really important, more than you think."

"What's so important about a jewel?" Shinji asked.

"It has the potential to give back life and the potential to take it away." the Emperor informed him. "That's why Gargoyle wants it. Kill all of humanity in one fell swoop."

"It can bring back the dead?" Shinji asked.

"Only if the will to live is strong enough." Neo said. "I'm very sorry, but I'm afraid you uncle has been dead long enough for it to not work."

'So it is my fault.' Shinji thought. "We need to go get it back."

"How? We don't even know where they are." Neo said.

"We have co-conspirators in SEELE." Kaji said. "I have word that Keel Lorenz is going to Greece."

"YES!" Shinji shouted. "And I told Fuyutsuki about Lorenz having it. We can kill two birds with one stone."

"That would work, but we only have one submarine left, sadly it's a prototype, and I don't know much about SEELE's tech, but the Neo-Atlanteans have a complicated sonar, not that it's stealthy anyway." Neo explained.

"I have a sub that can hide from sonars." Kaji said.

"We need a group of soldiers willing to fight for us." Neo said. "Luckily for you, I have just that."

They heard a call from Shinji's cell phone. "It's my parents!" Shinji laughed. "They can tell us where Lorenz going!" he answered the call. "Hello."

"Shinji! Thank the gods, you're okay." Yui said worried on the other side of the phone.

"Hi, mom. I'm fine." Shinji assured her.

"Good. I heard everything from Kaji." Yui said. "Is it true that you were forced to shoot Keiichi."

Shinji stood silent for a couple seconds before summoning the courage to speak. "Yes, it is. I am sorry."

"I understand. There was nothing you could do." Yui said. "Kill Keel Lorenz, he's the one behind all this, kill him, even if you have to kill your former comrades to do it."

"I will." Shinji swore. "Do you know where he is?"

"We can't say for sure where he is exactly." Yui said. "But your father found out where he is going now. Right off the coast of Greece."

"Near Greece? Why would he go there?" Shinji asked.

"Atlantis." Neo said. "They're going to Atlantis."

"What do you mean Atlantis?" Kaji asked.

"It was one of the three cities. Tartessos, another one of those cities, is our home." Neo said. "Until Gargoyle started to rebel and we had to leave. But they left the city, too, not to long ago. I don't know why."

"Why go there?" Shinji asked.

"To activate it." Neo said. "He's going to activate Tartessos!"

"What do he mean?" Kaji asked Shinji.

"I don't know, this is all news to me." Shinji said.

"Tartessos is more than a city, it's a space ship and there's weapons in them." Neo informed them. "There's at least three of them. The Red Noah in Atlantis and the Blue Noah in Tartessos. I don't know anything about the third one. The Red Noah sunk with Atlantis. The Blue Noah is alright, but if put into the wrong hands it could spell death for us."

"Did you get all that?" Shinji asked his mother.

"Yes. I'm sending a few workers that found out about Lorenz's plot." Yui said.

"Didn't you say that SEELE's the enemy?" The Emperor asked.

"We have other's who are willing to help us." Yui said. "I can ask 'Commander Ikari' to send them there."

Neo though about it. "Do it." Neo said.

"Are you sure." Shinji asked.

"It's do or die." Neo said. "I say we 'do'."

* * *

 _Leviathan, Cells_

Nadia, Jean, Marie, Captain Nemo, the Grandis Gang, even the cub were in cells. Nadia and Jean stood in a cell next to the other. They stood silent over what happened. "I know you want to say something." Nadia said to Jean.

"I do." Jean said. "I just don't know how to say it."

"It's alright. It's not you're fault or Shinji's." Nadia told him. They sat in silence until Nadia spoke again. "Do you know why Shinji keeps mispronouncing you name?"

"Why?" Jean asked wondering.

"Because, other than me, he never had any friends. He saw you as a friend, that's why he called you those names, he thought that was a thing." Nadia laughed.

Jean just chuckled. "Good to know."

"Shinji always stayed away from others, because he was scared of losing them." Nadia said to him more. "It was new territory for him and he didn't know what to do with it."

"When and if we get out of this, I'm going to call him Shingen just to see his face." Jean laughed then fell to silence. "I really am sorry about your Father."

"Thanks. I appreciate it." Nadia thanked him.

The door opened to reveal Electra, the traitor. "I have brought you food. You better thank me, cause I had to convince Gargoyle." Captain Nemo gave her a monstrous look. "Don't look at me like that. You would starve if it wasn't for me."

Nadia find whispered a word. "Why?" Electra heard it. "Why did you betray your friends? Why did you a part of my fathers death!? WHY DID YOU HAVE TO SHOOT SHINJI!?" Nadia shouted.

"I have my reasons. You may not accept it, but I am sorry, for everything." Electra said.

"What a load of crap!" Grandis said. "You're just as bad as Gargoyle if you think you can get away with this."

"Let me tell you something. There's no one to save you. Not the Emperor, not the Loyalist, and not Shinji." Electra said.

"You underestimate all of them." Nemo said. "The Emperor and his Loyalist are some of the toughest men I've seen and with Shinji on they're side, going by what I heard, we can see about that."

"Even with his help, the Neo-Atlanteans will defeat them." Electra said. "If you don't believe me, wait and see what happens." She left, leaving them alone with thier thoughts.

* * *

 _Agharta Docks_

A group of people were lined up. "They definitely got here fast. These are the specialists?" Neo asked.

"Yes, guaranteed." Kaji said. "You're here for a very important mission! One that could spell victory or death!" Kaji shouted at the group. "We are going to rescue some captives and annihilate the Neo-Atlanteans and SEELE! I know you considered them comrades, but after this, take that emotion out completely! Engineers! You are tasked to repair that sub!" Kaji ordered. "Soldiers! You are tasked to help out the Atlantean Loyalist when they fix that submarine! This will be our defining moment! Remember this! It's now or never!" The crowd cheered.

Neo was impressed. "Good speech."

"I will take the Hattori." Shinji said behind them. "There's no way the Atlanteans can find it."

"What are you planning?" Kaji asked.

"I'm going to get them out, give you a chance to go all out." Shinji said.

"Do you think you can use that vessel all by yourself?" Neo asked.

"I didn't say I'm going alone." Shinji said. "I'm going to need your help."

"I'm just an ruler, not a scout." Neo exclaimed.

"But you're familiar with the terrain." Shinji begged. "Or was I mistaken?"

"I am familiar with it, but I only been there once, before all this." Neo admitted.

"Then I need you to do me a favor. Let Kaji take command of the Nautilus II." Shinji said.

"Named after Nemo's ship?" He asked. "Fine. Just let me tell my men to follow his orders. At least, until I say otherwise."

"Fair enough." he smiled to the Emperor.

Later, Shinji was preparing to go down, waiting for the Emperor. "I told them everything. Are you sure this will work?"

"Yes, I'm connected to Kaji via radio." Shinji showed the radio. "I will tell him what to do when the Nautilus II's repairs are finished."

"This is a terrible idea." Neo started to laugh. "But like Kaji said, it's now or never." the Hattori launched under the sea. "I just hope these engineers are fast."

"They are the fastest in the world, the best of the best." Shinji said to him. "There's nothing they CAN'T fix. Let's save Nadia, Jean, and the others, even the Captain. TO ATLANTIS!"

* * *

 _Looks like Shinji formed a real army. An alliance of Atlantean Loyalist and SEELE rebels and both plan on saving the world. Will SEELE and the Neo-Atlanteans go down or will Neo give in, tossing his bloody crown?_


	9. Under the Sea

_Disclaimer: Evangelion and Secret of Blue Water belongs to Gainax. Paranoia Agent belongs to Madhouse._

* * *

 **Traitors of the Stars: Genesis**

 **Chapter 9: Under the Sea**

 _The Leviathan, close to Atlantis_

"My Lord, there's some SEELE forces closing in on the city." one of the Neo-Atlanteans said.

"I don't think they know where the machine." Gargoyle said. "Just find a way to get the Blue Water. Nothing else matters."

"Understood." the follower focused on the SEELE fleet.

"The Red Noah. One of the three weapons. Finally in my hand." Gargoyle thought out-loud.

"Aren't you forgetting about the army your fighting?" Electra asked.

He just laughed. "Like I said, the humans are weak. Even if their technology is on par with ours, they lack spirit. Captain Nemo is imprisoned, Emperor Neo is armyless, and Shinji is broken. Keel Lorenz is the only threat."

"He does have the Blue Water." Electra thought out-loud. "Is that the reason why he's a threat?"

"Yes." Gargoyle admitted.

"But what is he doing? What is he going to do?" Electra asked.

"Something different than what we are doing." Gargoyle said. "That much I do know."

* * *

 _The Hattori_

Shinji and the Emperor stood silent until Shinji spoke up. "Tell me something, what are you to Nadia anyway?"

Neo was shocked. "What brought this up?"

"I heard Gargoyle call her 'Princess' and I highly doubt it was used as an insult." Shinji explained.

"Cat's out of the bag." Neo half-joked. "She's my sister, the one I told you about. Her full name is Nadia La Arwall."

Shinji was speechless. "What about the Captain."

'Never thought I'd be calling him this again.' Neo thought "Eleusis La Arwall, my father."

Shinji chuckled. "And I'm guessing Neo isn't your real name either?"

"Correct." Neo admitted. "Name's Benusis La Arwall. But if you don't mind, I'd still like to be called Emperor Neo Icon Epiphanes, if you don't mind."

"Fine, but YOU have to tell them sooner or later." Shinji said.

"Alright." Neo agreed.

'Nadia is a princess.' Shinji thought. 'I'd always known she wasn't technically part of the family, but I never known of this.'

"I just hope your parents can provide more backup against SEELE." Neo said to him.

"There's no way they'd let us down." Shinji assured. "I'll get in contact with Kaji."

* * *

 _Agharta Docks_

Kaji answer his cell. "Shinji?"

"Yes." He heard Shinji's voice. "Any news on my mother and father?"

"As a matter of fact, just before you called. Yui told me that Gendo talked to the other branches of SEELE who were aware of what Lorenz is doing." Kaji said. "You remember Kyoko, right?"

"Yes, the commander of the SEELE European Branch, right?" Shinji asked.

"Surprised you remember her, that was years ago." Kaji was surprised. "Anyway, she contacted them and they told her everything about what happened. They'll be sending reinforcements."

"That's good to hear." Shinji said. "Is the Nautilus II fixed?"

"Not yet, but it's getting there." Kaji admitted.

"Okay." Shinji sighed. "Well, if there's anything else, tell me immediately."

"Understood." Kaji said as he ended the call. "Okay everyone, I want that sub fixed and back in the water! Remember, it's now or never!"

* * *

 _The Hattori_

Shinji smiled when the call ended. "Good news: the Nautilus II is nearly ready. Better news: My parents called reinforcements from SEELE."

Neo just nodded. "That's good. Lady luck is on our side for once." he said coldly.

Shinji noticed his tone. "You don't trust us, do you?" he asked.

"To be honest. Other then my father, we never really had any allies." Neo admitted. "He never did have any reason to leave, he just did his own thing. That was before I was rescued."

"Does he know who you are?" Shinji asked.

"I don't know." Neo said. "If anything, he's real good at hiding stuff, even his emotions when danger could be around the corner. I swear, he's a man who can't be broken."

"You think highly of him." Shinji noticed.

"Of course. If I'm supposed to be the heir of the throne, I needed to be good at making tough decisions." Neo said. "He always made the right decisions."

"When this is over, what do you plan to do?" Shinji asked.

Neo chuckled. "I'll probably give him back the throne. It was his for some time."

"Are you sure?" Shinji also asked.

"Of course I am. I'm not ready to be king yet." Neo said. "Just do me a favor. Keep everything you seen a secret to the other humans. The less people who know us, the better."

"Understood." Shinji agreed. "I'll tell them to not tell anyone. I'll just say that SEELE had a coup, they'll eat it up. How much further are we to Atlantis anyway."

"Not to far now." Neo said looking at the map. "Just around Crete."

* * *

 _The Leviathan, approaching Atlantis_

Gargoyle sat on the captain's chair on the bridge. 'I don't know what you're planing Lorenz. But mark my words I will bring peace to the world.'

Electra entered the bridge. "Is everything ready."

"Yes." Gargoyle said. "We will be docking in Atlantis any minute now. He will be no match for the fleet."

"That's very good to hear." Electra said.

The Leviathan approched the docks of Atlantis. Gargoyle found an interesting discovery. "An air dome? So anyone could come here." Gargoyle chuckled. "Approach the dock and lets go save the Atlantean civilization." Just then, an explosion was heard. It was from the inside. "There shouldn't be any weapons SEELE has that can pierce this machine." He looked at Electra. "You..."

"After giving the prisoners food, I went to the engine room, plant a bomb and waited for the right moment." Electra said.

"I didn't want to believe it. You wanted this to happen." Gargoyle said. "It's against my better judgement to hurt a woman." He punched her as hard as he could. "Sadly for you, I got rid of my better judgement years ago." Electra passed out. "Bring her to the torture room, so that I can kill her myself. Before that though, we need to find Lorenz. The survival of the Atlanteans is in the palm of his hand and time is not on our side."

* * *

 _The Leviathan, Cell Area_

They heard an explosion and shortly, the cell doors were open. "What happened?" Jean asked.

"An explosion." Grandis said. "But where did it come from?"

"You don't think that Electra did this?" Hanson asked.

"Yes." Captain Nemo said. "It came from the inside. Looks like she was waiting for the perfect oppertunity. We need to move while we still can."

Everyone started to leave except for Nadia. Jean and Marie noticed her. "Nadia, we have to go." Marie said.

"Just go." Nadia said quietly. "There's nothing left for me."

"That's ridiculous." Jean said. "You have us and Shinji. He's probably coming to get us now. If you don't join us, then what would we be fighting for. What would Shinji be fighting for."

"Just go." Nadia said, starting to get angry. "We are alone. Shinji's not coming."

* * *

 _The Hattori, Atlantean Docks_

Shinji saw the Leviathan. "That's It?"

Neo saw the sub. "No doubt about it." The Hattori got closer. "Before we go, tell me. Why are you helping us?"

"What do you mean?" Shinji asked.

"After everything you did, I just get past it and just pretend it didn't happen, but I can't do that." Neo explained. "So even after all that, why do you help us? And please don't say you want vengence for your uncle or saving my sister."

"What are you implying?" Shinji was getting worried.

Neo assured him. "I understand either one, but what I mean is, best case scenario: If we win, if you and you're allies help us win, what do you want?"

"I guess I can help you reclaim your old home." Shinji said. "Build it back up to the way it was and you can even reintroduce Nadia to her birthplace. Even if there is some chance that I may never see her again, it doesn't matter. Many cities were burned down at one point or another. Many people also left those cities, because of the same thing. Tartessos is no different. Just promise to never forget me." he said sentimentally.

"Wow. She really means that much to you, huh?" Shinji nodded as Neo asked that. "You're risking you not seeing her again, just so she can go home?"

"Yes. All I ask is that you don't forget me." Shinji asked.

Neo was excited to hear this. "Tell you what, if you... when you help rebuild the city, I'll make a statue of you." He patted him on the shoulder. "Hell, can even come visit whenever you want."

"Thanks." Shinji said with tears in his eyes. "I appreciate it."

"Don't give me that. Save it until after this is over." Neo smiled. "Now, let's save the world, brother."

Shinji smiled back. He didn't need no words to know what he meant.

* * *

 _Atlantis_

The Hattori rose from the entrance, shocking everyone there. "What the hell?" One Neo-Atlantean said.

"We've been followed?" Another said.

The hidden Captain Nemo took the opertunity to take the gun from one of the guard and shoot all of them in one fell swoop. The hatch opened to reveal Shinji Ikari and Emperor Neo. "Lots of blue here."

"Shinji!" Jean said running towards him. "It's good to see you! You need to talk to Nadia. She's in utter shock after what happened with..." He fell silent.

"Understood." Shinji said. "Where is she?"

"She's hiding behind the pillars over there." Jean pointed to the location. "Marie is with her, making sure she's not alone."

"Thanks." Shinji walked towards her.

"Wait." Shinji stopped. "She told me why you always say my name differently."

"You're not mad?" Shinji asked.

"No." Jean said. "Now get going. She needs you now more than ever."

Shinji walked behind the pillar Jean pointed. Sure enough they were there. "Marie."

"Shinji." Marie hugged him.

"I need to talk to Nadia for a bit. Go join Jean for now." He said. Marie left them alone. "Nadia. Look, I'm here. It's me, Shinji"

"Shinji's not coming." Nadia said, almost in a trance. "We're alone."

Shinji frowned. "I know I failed you. I know a made a huge mistake taking your necklace. It was the only thing you had to remember the old life. The life you had before you met me."

Nadia looked up at him. "Shinji?"

"I put my duty over my family. Waiting for that oppertunity to take it. I put everyone's lifes at stake, I put Uncle Keiichi's life at stake, because of my greed." Shinji started to cry. "I want to ask forgiveness, but I can't even do that. So let me get back your necklace, consider this my last chance."

Nadia hugged him. "I forgive you."

* * *

 _The final battle is close at hand. Shinji is the only one who can stop Keel Lorenz. The Neo-Atlanteans are not far behind. The end of everything._


	10. Masters and Student

_Disclaimer_ : _Evangelion and Secret of Blue Water belongs to Gainax. Paranoia Agent belongs to Madhouse._

* * *

 **Traitors of the Stars: Genesis**

 **Chapter 10: Masters and Student**

 _Tower of Babel_

Keel Lorenz and his loyalist forces stared at the tower. "So the Tower exist after all." He saw a control panel in front of it and noticed a diamond shaped hole to insert the Blue Water. "Everyone! You have done an exceptional job finding this place. I relieve you of your duties!" He used his machine gun to kill all of his forces. They screamed for mercy, but it was for naught. He then saw the spirits of the men he killed go into the Blue Water. 'What is this? Is this some kind of Soul Gem?' He was shocked, he then looked at the architecture "This place as alot of blood on it, doesn't it?" He ask himself. He then found some hieroglyphs showing the Arwall Family crest and some kind of oni next to it. "This isn't possible." He coundn't help but laugh. "I really made a mess of things now. But I'm willing to bet you don't care, do you."

* * *

 _Atlantis Docks_

Shinji and Nadia walked down to the others. "I'm going after Keel Lorenz." Everyone, even Nadia, was shocked when they heard Shinji said that.

"Shinji, it's a suicide mission. Not only is there a army of SEELE soldiers with him, there's also an army of Neo-Atlanteans between us and him." Nemo said.

"Don't worry. Shinji has plans." Neo told the Captain. "I trust him."

"I need to do this. I'm the reason this happened." Shinji said. "I need to be the one that takes him down."

"Why do this?" Nemo asked Shinji. "Why risk your life for our sake."

Shinji was deep in thought until he turned to Nadia. "Do you need a reason to help a family member?"

"I see." Nemo said.

"The best techniques are passed on by the survivors." Shinji said. "I will fight Lorenz. Consider it my reason to help you. So you can survive."

Nemo was awestruck by this. He was right, they had nothing to do with all this until now. "Alright, we need a distraction to help Shinji through the Neo-Atlanteans, so he can have a clear shot to Lorenz."

"I'm in." Neo said.

"I usually don't like being caught, but if it's for the good of humanity." Grandis said.

"We're right behind you." Hanson said.

"You two would still stay with me?" Grandis asked. "Even at the end?"

"Of course. You took us in when everyone else shuned us for no reason." Sanson said. "You are the only one we'll follow."

"Thanks." Grandis said.

"I'm also in." Nadia said.

"No. The last thing I need is another dead family member." Shinji told her.

"Shinji, he killed my father." Nadia said really angrily at Shinji. "If anyone deserves death it's him."

Shinji took a moment before he spoke. "Understood." He then looked at Jean. "Jean, can you take care of Marie?"

Jean nodded. "You can count on me, Shaun."

"It's..." Shinji started to say, but stopped when he got it. "I'm counting on you, buddy."

"The Nautilus II is the only safe haven." Nemo said. "I'd hold out there."

"Let's go, Marie." Jean said.

"Shinji!" Marie shouted. "Promise me you'll save us."

Shinji patted Marie on the head. "That's my intention."

"Alright, Shinji, there's some shadows close to the pillars, use them to your advantage." Nemo said to Shinji.

"Understood, Captain." Shinji said.

"I highly doubt we can get Gargoyle here, considering he's going after Lorenz." Neo said.

"True." Nemo calculated. "That's why we need a distraction. Get some of his forces to be cut off."

"I'll sneak up on them and follow them." Shinji stated.

"Then take this." Neo gave him a sub-machine gun. "Normally I wouldn't give something like this to you. But you were a SEELE Soldier, you know Lorenz better than anyone else here." He put his hand on his shoulder. "Now get out of here."

Shinji ran towards the shadows and continued.

* * *

 _Atlantis Corridors_

Gargoyle walked through the halls until he heard gun shots. "Ten of you, come with me. Everyone else, take care of that." He continued to walk 'Looks like Nemo is fighting back. Not that it matters.' He just sighed. "Goodbye, old friend. I'll be sure to put your name in the archives... as a traitor."

All of a sudden, bullets were raining down on his forces, killing everyone but him. "The only traitor here is you, Master Fuyutsuki." A familiar voice called to him.

'There's only one person that calls me that.' Gargoyle thought. "Come out, Shinji or am I speaking to a ghost?"

Shinji came from the shadows. "I have to give you credit. Without your training, I would have ended in a despression based coma. So being here now, it's all you I have to thank."

"You think because I helped you, you became a better man?" Gargoyle asked. "I had to go undercover from that baffoon and I have been waiting for ten years, waiting for the oppertunity to strike. Looking for the Blue Water was my ultimate goal. If anyone finds out what it's capable of, we'll all die."

"How is it different than what you're doing?" Shinji asked.

"Humans destroy everything! If they see something they don't like, they kill it! If there's one thing I can do, it's free everything from their grasp!" He yelled.

"So you're telling me, 'we should all die, because of what some of us are doing.'" he asked more.

"Evil begets evil!" Gargoyle was ranting more. "Not long, the only thing the earth will be is a huge desert, nothing to give life to! Even the underwater plants and animals won't be immune!"

"You're right." Shinji said. "There are some scumbags on earth. Maybe more if it goes unopposed." Shinji was lost in thought, looking at his gun. "But..." He then shot him in the legs and arms. Gargoyle was screaming in pain. "There won't be anyone to stop that, if you do this. Goodbye, Master." He walked away from him. "I'll let the Atlantean Loyalist have their way with you."

"Shinji! You son of a bitch!" Gargoyle yelled. "The Atlantean Loyalists are dead!"

"Oh, I wouldn't count on that." His phone beeped. "This is Shinji."

"The Neo-Atlanteans have been neutralized." Kaji said over the phone.

"Glad to hear it." Shinji said. "Can you put Nadia on?"

"Sure." Kaji handed Nadia the phone.

"Shinji?" Nadia asked. "Are you there?"

"Yes and I have a gift for you." He walked back to the broken body of Gargoyle. "Give her a quick shout-out." Shinji stepped on one of his injured limbs, causing him to scream. "Did you get that."

"Yes." Nadia said. "Hoped you left some for me."

"Don't worry, I left you best part. He's not going anywhere." Shinji looked at Gargoyle again. "I made sure of that."

"You better get going then." she said. "Lorenz is still out there."

"Understood." Shinji walked towards the direction of the throne room.

* * *

 _Atlantean Throne Room_

Shinji entered the room and saw the Tower of Babel. "Whoa." He was in shock at the machine.

"The Tower of Babel." Shinji turned to see Keel Lorenz and immediatly aimed the gun at him. "I was expecting the Neo-Atlanteans, but your even better."

"What are you talking about?" Shinji asked.

"I was planning to use the Blue Water as leverage to get Nadia from them." Lorenz said. "But from what I discovered, only the blood from the Royal Family can be used for it to activate the Tower."

"What does this have to do with me?" Shinji asked.

Lorenz pointed to the wall with the hieroglyphs. "Take a look for yourself."

Shinji saw the wall then saw the crest. "This can't be."

"It's your family crest. YOUR blood can be used in a different way." Lorenz said. "The blood of the Royal Family can be used to kill every being that has the slightest human DNA. Yours on the other hand, the Tower can be used to open a portal."

Shinji lowered the gun. "What's your gain?"

"To help the weak, to help humanity." Lorenz looked at the tower. "And hopefully, to find them a true home."

"We're happy where we are." Shinji said.

"Are you?" He asked. "Seeing people get killed? Seeing people die due to disease and sickness? Seeing homes get destroyed? Is that really the world you want to stay in?"

Shinji was lost in thought. "There are some people who are willing to kill just to get a laugh." Shinji admitted. "But as long as there's one man who can save people, there's always hope."

Lorenz chuckled. "I'll spare you the times I told myself that."

"Give me the Blue Water." Shinji pointed the gun at him again.

"Or what?" he asked. "How about this? Put the gun away and I'll give you the Blue Water."

Shinji puts the gun away and pointed to the ground. "Put it on the floor."

Lorenz moved closer to Shinji, stopped midway, and placed it down, moving back after. "There you go."

He moved closer to the Blue Water and picked it up. "Now listen, If you come peacefully I can encourage them to get you off light." Shinji offered.

"To be honest. I have you right where I want you." A knife was close to Shinji's throat. Lorenz was the man holding the knife. "The wonders of holograms." He said as the hologram of him disappeared.

He took the gun from Shinji. "How? Holograms can't carry objects."

"I used a special device that uses things to give off the appearance of levitation." He proceeded to the Tower with Shinji. "I was planing to use this tactic against the Neo-Atlanteans, but like I said, you were better."

Shinji noticed the dead bodies close to the Tower. "What the hell is this?"

"These men served me well." Lorenz said. "Gave them an early retirement." He continued walking until he got to the control panel. "Now bare witness to the power!" Lorenz inserted the Blue Water in the panel. "That will save everyone!" He grabbed Shinji's hand, removed the knife from his neck, and sliced his hand. "Open the door to paradise."

The blue water glowed green. The tower activated and, from there, a portal opened. "What is this?!" Shinji asked.

Lorenz laughed. "This, my friend, is the portal, the door, to everyman's desire!" He basked in his victory. "Noah's Ark!"

"Noah's Ark?" Shinji was stunned.

"The same ship from the story." Lorenz cheerfully said. "And you are going to be the first to experiance it."

"No." Shinji said. "Not now or ever. I've seen this done in several stories. We're happy where we are and if we have to leave, we'll leave by our own accord."

"This is our destiny. Do you think I would go through all this just to have power?" Lorenz asked.

"You're trying to force us to do things we don't want to do yet." Shinji retorted. "That sounds like power."

"You're family's been with me since we had to clean up that mess ten years ago." Lorenz reminded him. "You had it right then."

"Keyword being 'then'." Shinji pointed out. "NOW. Now, I'm going to kill you."

"Do you honestly think you can take me on?" Lorenz asked, laughing at him. "I was in three wars in a row! I was tortured to death by all those enemies! They all tried to crack me for information, all ending in failure. I became a stronger man from those events. What do you have?"

"YOUR TRAINING!" Shinji yelled.

* * *

 _Tower of Babel. Royal Family: Glows Red, World destruction. Ikari Clan: Glows Green, A portal to another plane of existance._

 _The Ikari Clan and the Royal Family. Connection: Questionable._

 _"What the Hell?"_


	11. Things To Come

_Disclaimer: Evangelion and Secret of Blue Water belongs to Studio Gainax. Paranoia Agent belongs to Studio Madhouse._

* * *

 **Traitors of the Stars: Genesis**

 **Chapter 11: Things To Come**

 _Tower of Babel_

Shinji got rid of his weapons. "I want to fight you, mano a mano."

Lorenz did the same. "Alright. Your funeral."

Shinji and Lorenz ran towards each other. Lorenz punched Shinji, which he then followed with a leg sweep. Shinji kicked him as he got up and elbowed him in the face. They stared at each other intensely. Lorenz cracked his knuckles, ran towards Shinji, and punched him in the gut. Shinji then chopped his neck, causing Lorenz to stagger. Shinji shouted as he punched him repeatedly. Lorenz countered with a chokehold.

"I told you, if you think you can defeat me, let alone kill me, you may as well be dead." Lorenz taunted.

Shinji broke out after kicking Lorenz in the groin. "Then I'll think of it as a tie."

* * *

 _Ten Years Ago_

 _"I want to know all there is to know about this tower." Lorenz said to his soldiers. "If you find even the smallest thing, tell me. If you don't have anything, don't bother showing up."_

 _"Yes sir." the soldiers left the office._

 _"I'm surrounded by idiots." Lorenz complained to himself._

 _Many days has past. Lorenz has not heard anything about the Tower of Babel... until now._

 _"Sir. Sir, I got good information." A soldier said as he handed the information._

 _Lorenz saw the documents. "Where did you get this."_

 _"In Spain, by the coast." the soldier explained._

 _"Hmm." Lorenz looked at the language on the picture. "Has these been translated?"_

 _"Yes, sir." the soldier said. "It says something about a royal family."_

 _"Interesting." Lorenz looked at the documents._

 _"With respect, sir. That's not what I find interesting." he said._

 _"What do you mean." Lorenz asked._

 _"It also mentions the Ikari clain from Japan." the soldier said. "They have a mysterious history, but they're still around. Wouldn't surprise me if they don't know this now."_

 _'What the hell?' He thought in disbelief "That event happened just recently, right?" Lorenz asked._

 _"Yes, why?" the soldier asked._

 _"We're going to help them out." he smiled._

* * *

 _Tower of Babel_

"Tell me, why me?" Shinji asked. "Why my family? This place is not even mine. Why even involve us?!"

"You still don't get it." Lorenz taunted. "Your family and the Royal Family are connected. They used the Tower to end the world, in case things got too chaotic. That is until the Emperor at the time ascended from the ocean and met a family, your family, the Ikari Clan. That was during the time of the Genpei War." he explained to Shinji. "The Ikari Clan has a power, passed down from the war god Bishamonten, that can fight like berserkers, making the enemies they fight think they were fighting demons."

"I already know that, 'General'." Shinji said.

"It's that power that can be used the tower in a different way, as a gateway to a portal." Lorenz smirked. "That is why the Ikari Clan was essential to the Atlanteans. I admit I found this out because of the hieroglyphs over there." He pointed to the wall. "I thought the Blue Water was all I wanted. I was planning to use your mother, but now that your here, alive, that's unnessesary."

"Then why kill the Atlanteans? They weren't doing anything! My uncle died because of you!" Shinji shouted.

"Now, hold on." Lorenz tried to calm him down. "His death wasn't intended. You can blame Fuyutsuki for that. I can bring him back, but only if you join my cause. Help bring us to a better life." He reached his hand.

"What of the Atlanteans?" Shinji asked.

"There's some things that we need to let go of." Lorenz said. "I'm sorry."

Shinji looked at Lorenz's eyes, he was sincere about helping humanity. "I would love to join you." But he was also willing to kill the Atlanteans. "But I won't allow you to kill the Atlanteans! If that's the price, forget it."

"You little shit!" Lorenz charged at him and started choking him. "So you think you can walk away from fate? I've challenged fate far too many times! Accepting that and showing the way is the mark of being a true goddamned hero."

Shinji's eyes started glowing red, he started to struggle with Lorenz, and threw him off. "You've met with a terrible fate, haven't you?" Shinji laughed hysterically, turning his head around to show his wide opened eyes glowing a bright red and a grin that looks like he's about to eat Lorenz.

"What the hell?" Lorenz was in shock. "What are you."

Shinji laughed again. "I am your death!" Lorenz punched him in the face. "You shouldn't have done that." Shinji punched Lorenz sending him flying. "I win." He grinned as he walked towards him. "Go to sleep." He said before he gauged out his eyes with his thumbs. Lorenz screamed in pain. "That'd take care you." Shinji looked at the Tower and went to the control panel. He tried to pry the Blue Water out, but it failed. He decided to break it. The Blue Water fell out, but the Tower of Babel and the throne room started to collapse. "It's over." Shinji started to laugh again. "They're saved."

* * *

 _Atlantis Corridors_

The group of Atlantean soldiers came up to Gargoyle, maskless. "We got him, sir." One of them said to the Emperor.

"Very good." Neo smiled. "Get a stretcher for him."

"No!" Nadia said. "We should kill him now, while we still can."

"He will recieve punishment." Neo said. "He does deserve death, it doesn't mean we should stoop to his level."

Nadia looked at Gargoyle. "I should kill you, right now!"

"I help Shinji train to become a true soldier." Gargoyle said. "It was a test to see if he can take a life without remorse." Gargoyle chuckled. "He succeeded."

Nadia punched him in the face repetedly. "YOU MONSTER. YOU EVIL MONTSER!"

The Atlanteans had to restrain her. "That's enough." Captain Nemo said.

They heard rubble in the distance. "Looks like the student has surpassed the master."

"Shinji." Nadia said silently.

"Stay here." Neo said to everyone before going on ahead to find Shinji.

* * *

 _Collapsed Throne Room_

Shinji layed under the rubble. 'So this is how I die.' He was prepare to take his last breath. 'At least I'll die a hero.' The Blue Water fell from the rubble and onto Shinji. "What...?" A blinding flash came from it when it made contact to Shinji.

 _Shinji walked through the empty blue halls. "What is this? Is this the tunnel that they all say?"_

 _"No." Said a soothing female voice. "Your spirit is in the blue water."_

 _"What do you mean?" Shinji asked. "Who are you?"_

 _"Don't worry. It's only temporary." The voice said. "I've only called you in here, because I'm warning you about what's to come."_

 _"I'm a little lost here." Shinji said. "I know you must think I'm some hero. But, I'm not. Not really. Everything I've done was the benefit of the Neo-Atlanteans and SEELE. My uncle died and I pulled the trigger. I'm a walking timebomb." Shinji started to cry._

 _"I agree." The voice said. "And you exploded right in the enemy's face." Shinji looked up. "You are also the ideal hero the Atlanteans were looking for." A vision opened up to him. "This is Tartessos in the near future."_

 _He saw a large Atlantean town below him. "It's beautiful." He turned his head and saw a statue of himself. His eyes were wide with awe._

 _"Only because you made it happen." The voice mentions. "And your parents are the new leader of SEELE. I'm sure they'll be in touch with us. Now that your 'cousin' is the Princess of Tartessos."_

 _"What do you want to warn me about?" Shinji asked._

 _The voiced waited for a moment before speaking. "An ancient evil is approaching. I don't know when it will come, but it will come. They're call Angels."_

 _"Angels?" Shinji asked. "They exist."_

 _"Yes." The voice said. "Although they're not all they claim to be. I know someone who might be willing to help you. But until then, fight them."_

 _"I will." Shinji said._

 _"Also, and this will pain me the most to say, I want you to fake your death to your cousin and the Atlanteans." The voice said._

 _"Why? Don't they want to see their hero still alive?" Shinji asked her._

 _"I know that's the case, but strong beings are coming." She said. "If they found out about you and her being connected, they might use her to get to you. It's best if you die a hero. Tell the Emperor and the Captain, no one else."_

 _"Understood." Shinji said._

 _"If somehow she does find out you survived, tell her you died to be a hero, please." The voice pleaded._

 _"I can do that. Tell me, who are you?" Shinji asked. "I know your not telling me all this for your benefit."_

 _The voice chuckled. "Let's just say, there's some questions that deserved to be unanswered for now."_

 _Shinji shook his head. "Of course we need a bodyless voice to be as cryptic as possible."_

 _"Trust me. You'll learn, in time." The voice assured him._

 _"Will I see you again?" Shinji asked._

 _"When this is all over." a portal opened in front of Shinji. "Go now, and prepare to save the world."_ _Shinji entered the portal._

He gasped as he came to life. "Shinji!" The Emperor said as he found him. "Thank the gods, you're okay."

"Neo?" Shinji said. "What's happening."

"I feared the worst. I didn't see you, so I thought you were under the rubble." Neo said. "It's a miracle that you survived."

"I had this with me." Shinji took the Blue Water. "I was dying when..." He changed the subject. "I need you to keep my survival a secret."

Neo was shocked. "Why? The people deserves to know. Nadia deserves to know."

"There's a greater menace coming." Shinji said. "Not to mention, that portal was opened long enough. Something must have come out."

"What are you saying?" Neo asked.

"He said that the blood of the Ikari Clan has the power to use the Tower as a prison." Shinji explained. "One may have gotten out. You have to keep it a secret from the Atlanteans."

"Fine. I'll tell my father, but no one else." Neo said. "Make sure he doesn't make that mistake. I'll give the position of emperor back to him."

"Are you sure?" Shinji asked.

"All I did when we gained allies was question their motives." Neo bowed his head. "I saw you as an exception, I saw myself in you. I don't deserve to be ruler."

"I hope you make peace with it." Shinji said.

"I will. Now let's get you home." Neo said. "I'll call a stretcher. I hope you have something to fake your death."

"I do." He took out a pill. "It's called a fake death pill, it's diffenatly going to help me. I have a revival pill ready, so don't worry."

"Okay, see you on the other side, brother." Neo said.

Shinji swallowed the pill and closed his eyes.

* * *

"The Neo-Atlanteans were disolved. Gargoyle was trialed and executed for his crimes. Neo gave his position to Nemo publicly. SEELE was converted to NERV with Gendo and Yui Ikari as the new leaders. Nadia the princess of Tartessos found out about her true father, it took a while to sink in, but ultimately, she accepted her father. I on the other hand were looking for allies to help with the arrival of what we know now as angels. That was my story, a story that wasn't suppose to happen, but did." Shinji ended the story.

"That's alot more complicated than I thought it would be." Touji said.

 _To be concluded..._

* * *

 _That's the end of the prequel story. Hope you enjoyed it._


End file.
